Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

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Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Henrik Bengtsson
Hi,

first of all, for this chip type you need to specify:

bc <- GcRmaBackgroundCorrection(csR, type="affinities");

Moreover, you cannot use the custom CDF in the
GcRmaBackgroundCorrection step, and have to do the follow workaround
illustrated in the below example:


library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Affymetrix-Tissues";
chipType <- "MoEx-1_0-st-v1";

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR");
print(cdf);
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
print(csR);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# gcRMA-style background correction
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Currently, you must use the standard CDF file.
cdf <- getCdf(csR);
cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
setCdf(csR, cdfS);
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
print(csB);
# Now, use the custom CDF in what follows
setCdf(csB, cdf);
print(csB);

Yes, those last steps are rather confusing - we're working on updating
the code so you don't have to do that yourself.

FYI, the above solution/workaround was resolved in thread 'GCRMA
normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
http://goo.gl/cniq.

Hope this helps

/Henrik

On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
<[hidden email]> wrote:

> Hi All,
> I am trying to normalize a mouse exon array dataset using GCRMA
> normalization technique. I have exactly followed all the necessary steps for
> storing the dataset and the cdf file. the code and the output I am using are
> as follows:
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.affymetrix")
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.cn")
>
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>
> dataSet <- "Exon Data" [the path in the working directory is rawData/Exon
> Data/MoEx-1_0-st-v1/*.CEL files]
>
> chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
> [converted to binary using convertCdf command]
>
> print(cdf)
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/MoEx-1_0-st-v1
>
> Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>
> Filesize: 30.53MB
>
> Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 2560x2560
>
> Number of cells: 6553600
>
> Number of units: 17831
>
> Cells per unit: 367.54
>
> Number of QC units: 1
>
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>
> print(csR)
>
> AffymetrixCelSet:
>
> Name: Exon Data
>
> Tags:
>
> Path: rawData/Exon Data/MoEx-1_0-st-v1
>
> Platform: Affymetrix
>
> Chip type: MoEx-1_0-st-v1
>
> Number of arrays: 7
>
> Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
> P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>
> Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>
> Total file size: 440.55MB
>
> RAM: 0.01MB
>
> cdf <- getCdf(csR)
>
> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>
> setCdf(csR, cdfS)
>
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>
> print(bc)
>
> GcRmaBackgroundCorrection:
>
> Data set: Exon Data
>
> Input tags:
>
> User tags: *
>
> Asterisk ('*') tags: GRBC
>
> Output tags: GRBC
>
> Number of files: 7 (440.55MB)
>
> Platform: Affymetrix
>
> Chip type: MoEx-1_0-st-v1
>
> Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
> indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
> opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>
> Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>
> Is done: FALSE
>
> RAM: 0.00MB
>
> csB <- process(bc, verbose=verbose)
>
> 20100923 13:24:12|Background correcting data set...
>
> 20100923 13:24:12| Computing probe affinities...
>
> 20100923 13:24:12|  Computing GCRMA probe affinities for 1257006 units...
>
> 20100923 13:24:12|   Identify PMs and MMs among the CDF cell indices...
>
>      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>
>        Mode   FALSE    TRUE    NA's
>
>     logical  334476 4931683       0
>
> 20100923 13:25:57|    MMs are defined as non-PMs
>
> 20100923 13:25:57|    Number of PMs: 4931683
>
> 20100923 13:25:57|    Number of MMs: 334476
>
> 20100923 13:25:57|   Identify PMs and MMs among the CDF cell indices...done
>
> 20100923 13:25:57|   Reading probe-sequence data...
>
> 20100923 13:25:57|    Retrieving probe-sequence data...
>
> 20100923 13:25:57|     Chip type (full): MoEx-1_0-st-v1
>
> 20100923 13:25:57|     Locating probe-tab file...
>
> 20100923 13:25:57|      Chip type: MoEx-1_0-st-v1
>
> Error in list(`process(bc, verbose = verbose)` = <environment>,
> `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = <environment>,
>  :
>
>
>
> [2010-09-23 13:25:57] Exception: Found probe-tab file only by means of
> deprectated (v1) search rules:
>
>   at throw(Exception(...))
>
>   at throw.default("Found probe-tab file only by means of deprectated (v1
>
>   at throw("Found probe-tab file only by means of deprectated (v1) search
>
>   at method(static, ...)
>
>   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>
>   at method(static, ...)
>
>   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
>
>   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>
>   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>
>   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
>
>   at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
>
>   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
>
>   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>
>   at do.call("bgAdjustGcrma", args = args)
>
>   at process.GcRmaBackgroundCorrection(
>
> 20100923 13:25:57|     Locating probe-tab file...done
>
> 20100923 13:25:57|    Retrieving probe-sequence data...done
>
> 20100923 13:25:57|   Reading probe-sequence data...done
>
> 20100923 13:25:57|  Computing GCRMA probe affinities for 1257006
> units...done
>
> 20100923 13:25:57| Computing probe affinities...done
>
> 20100923 13:25:57|Background correcting data set...done
>
> Could anyone please enlighten me with the type of the error? I will be
> highly obliged if anyone please help me with this problem.
>
> Thank you.
>
> Prithish Banerjee.
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Prithish Banerjee
Respected Dr Bengtsson,

My codes and outputs are as follows:

> hbInstall("aroma.affymetrix")
> hbInstall("aroma.cn")
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE); 
> dataSet <- "Exon Data"
> chipType <- "MoEx-1_0-st-v1"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
> print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags: 
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15 P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
> cdf <- getCdf(csR)
> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
> setCdf(csR, cdfS)
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
> print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags: 
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm", indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities", opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
> csB <- process(bc, verbose=verbose)
20100927 16:31:40|Background correcting data set...
20100927 16:31:40| Computing probe affinities...
20100927 16:31:40|  Computing GCRMA probe affinities for 1257006 units...
20100927 16:31:40|   Identify PMs and MMs among the CDF cell indices...
     logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
       Mode   FALSE    TRUE    NA's 
    logical  334476 4931683       0 
20100927 16:33:30|    MMs are defined as non-PMs
20100927 16:33:30|    Number of PMs: 4931683
20100927 16:33:30|    Number of MMs: 334476
20100927 16:33:30|   Identify PMs and MMs among the CDF cell indices...done
20100927 16:33:30|   Reading probe-sequence data...
20100927 16:33:30|    Retrieving probe-sequence data...
20100927 16:33:30|     Chip type (full): MoEx-1_0-st-v1
20100927 16:33:30|     Locating probe-tab file...
20100927 16:33:30|      Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = <environment>, `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = <environment>,  : 
  
[2010-09-27 16:33:30] Exception: Found probe-tab file only by means of deprectated (v1) search rules: 
  at throw(Exception(...))
  at throw.default("Found probe-tab file only by means of deprectated (v1
  at throw("Found probe-tab file only by means of deprectated (v1) search
  at method(static, ...)
  at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
  at method(static, ...)
  at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
  at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = 
  at getProbeSequenceData(this, safe = safe, verbose = verbose)
  at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
  at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
  at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
  at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1", 
  at do.call("bgAdjustGcrma", args = args)
  at process.GcRmaBackgroundCorrection(
20100927 16:33:30|     Locating probe-tab file...done
20100927 16:33:30|    Retrieving probe-sequence data...done
20100927 16:33:30|   Reading probe-sequence data...done
20100927 16:33:30|  Computing GCRMA probe affinities for 1257006 units...done
20100927 16:33:30| Computing probe affinities...done
20100927 16:33:30|Background correcting data set...done
> traceback()
17: throw.Exception(Exception(...))
16: throw(Exception(...))
15: throw.default("Found probe-tab file only by means of deprectated (v1) search rules: ", 
        pathname)
14: throw("Found probe-tab file only by means of deprectated (v1) search rules: ", 
        pathname)
13: method(static, ...)
12: AffymetrixProbeTabFile$findByChipType(chipType, what = what, 
        ...)
11: method(static, ...)
10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = less(verbose, 
        100))
9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = verbose)
8: getProbeSequenceData(this, safe = safe, verbose = verbose)
7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., 
       verbose = less(verbose))
6: computeAffinities(cdf, paths = probePath, ..., verbose = less(verbose))
5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1", 
       verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL, 
       typesToUpdate = "pm", indicesNegativeControl = NULL, affinities = NULL, 
       type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE, 
       gsbParameters = NULL, .deprecated = FALSE)
4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1", 
       verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL, 
       typesToUpdate = "pm", indicesNegativeControl = NULL, affinities = NULL, 
       type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE, 
       gsbParameters = NULL, .deprecated = FALSE)
3: do.call("bgAdjustGcrma", args = args)
2: process.GcRmaBackgroundCorrection(bc, verbose = verbose)
1: process(bc, verbose = verbose)
> sessionInfo()
R version 2.11.1 (2010-05-31) 
x86_64-apple-darwin9.8.0 

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7        affxparser_1.20.0     
 [4] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1    
 [7] matrixStats_0.2.1      R.rsp_0.4.0            R.filesets_0.9.0      
[10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.2         
[13] R.oo_1.7.4             R.methodsS3_1.2.1     

loaded via a namespace (and not attached):
[1] tools_2.11.1

The working directory is desktop and the path for the cdf file and the raw data is as follows:

/Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf ( I have several other cdf files like MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf and MoEx-1_0-st-v1.cdf in the same directory.) 

/Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/
DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
DK Litter D15 P2_(MoEx-1_0-st-v1).CEL
DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL 
DK Litter D15 P3_(MoEx-1_0-st-v1).CEL
DK Litter D15 P6_(MoEx-1_0-st-v1).CEL
DK Litter D15 P14_(MoEx-1_0-st-v1).CEL

Moreover I am following the thread and implementing the code you suggested there but it is not working with my dataset. Please help.

Thank you,

Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.


On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson <[hidden email]> wrote:
Hi,

first of all, for this chip type you need to specify:

bc <- GcRmaBackgroundCorrection(csR, type="affinities");

Moreover, you cannot use the custom CDF in the
GcRmaBackgroundCorrection step, and have to do the follow workaround
illustrated in the below example:


library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Affymetrix-Tissues";
chipType <- "MoEx-1_0-st-v1";

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR");
print(cdf);
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
print(csR);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# gcRMA-style background correction
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Currently, you must use the standard CDF file.
cdf <- getCdf(csR);
cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
setCdf(csR, cdfS);
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
print(csB);
# Now, use the custom CDF in what follows
setCdf(csB, cdf);
print(csB);

Yes, those last steps are rather confusing - we're working on updating
the code so you don't have to do that yourself.

FYI, the above solution/workaround was resolved in thread 'GCRMA
normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
http://goo.gl/cniq.

Hope this helps

/Henrik

On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
<[hidden email]> wrote:
> Hi All,
> I am trying to normalize a mouse exon array dataset using GCRMA
> normalization technique. I have exactly followed all the necessary steps for
> storing the dataset and the cdf file. the code and the output I am using are
> as follows:
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.affymetrix")
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.cn")
>
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>
> dataSet <- "Exon Data" [the path in the working directory is rawData/Exon
> Data/MoEx-1_0-st-v1/*.CEL files]
>
> chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
> [converted to binary using convertCdf command]
>
> print(cdf)
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/MoEx-1_0-st-v1
>
> Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>
> Filesize: 30.53MB
>
> Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 2560x2560
>
> Number of cells: 6553600
>
> Number of units: 17831
>
> Cells per unit: 367.54
>
> Number of QC units: 1
>
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>
> print(csR)
>
> AffymetrixCelSet:
>
> Name: Exon Data
>
> Tags:
>
> Path: rawData/Exon Data/MoEx-1_0-st-v1
>
> Platform: Affymetrix
>
> Chip type: MoEx-1_0-st-v1
>
> Number of arrays: 7
>
> Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
> P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>
> Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>
> Total file size: 440.55MB
>
> RAM: 0.01MB
>
> cdf <- getCdf(csR)
>
> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>
> setCdf(csR, cdfS)
>
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>
> print(bc)
>
> GcRmaBackgroundCorrection:
>
> Data set: Exon Data
>
> Input tags:
>
> User tags: *
>
> Asterisk ('*') tags: GRBC
>
> Output tags: GRBC
>
> Number of files: 7 (440.55MB)
>
> Platform: Affymetrix
>
> Chip type: MoEx-1_0-st-v1
>
> Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
> indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
> opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>
> Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>
> Is done: FALSE
>
> RAM: 0.00MB
>
> csB <- process(bc, verbose=verbose)
>
> 20100923 13:24:12|Background correcting data set...
>
> 20100923 13:24:12| Computing probe affinities...
>
> 20100923 13:24:12|  Computing GCRMA probe affinities for 1257006 units...
>
> 20100923 13:24:12|   Identify PMs and MMs among the CDF cell indices...
>
>      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>
>        Mode   FALSE    TRUE    NA's
>
>     logical  334476 4931683       0
>
> 20100923 13:25:57|    MMs are defined as non-PMs
>
> 20100923 13:25:57|    Number of PMs: 4931683
>
> 20100923 13:25:57|    Number of MMs: 334476
>
> 20100923 13:25:57|   Identify PMs and MMs among the CDF cell indices...done
>
> 20100923 13:25:57|   Reading probe-sequence data...
>
> 20100923 13:25:57|    Retrieving probe-sequence data...
>
> 20100923 13:25:57|     Chip type (full): MoEx-1_0-st-v1
>
> 20100923 13:25:57|     Locating probe-tab file...
>
> 20100923 13:25:57|      Chip type: MoEx-1_0-st-v1
>
> Error in list(`process(bc, verbose = verbose)` = <environment>,
> `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = <environment>,
>  :
>
>
>
> [2010-09-23 13:25:57] Exception: Found probe-tab file only by means of
> deprectated (v1) search rules:
>
>   at throw(Exception(...))
>
>   at throw.default("Found probe-tab file only by means of deprectated (v1
>
>   at throw("Found probe-tab file only by means of deprectated (v1) search
>
>   at method(static, ...)
>
>   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>
>   at method(static, ...)
>
>   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
>
>   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>
>   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>
>   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
>
>   at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
>
>   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
>
>   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>
>   at do.call("bgAdjustGcrma", args = args)
>
>   at process.GcRmaBackgroundCorrection(
>
> 20100923 13:25:57|     Locating probe-tab file...done
>
> 20100923 13:25:57|    Retrieving probe-sequence data...done
>
> 20100923 13:25:57|   Reading probe-sequence data...done
>
> 20100923 13:25:57|  Computing GCRMA probe affinities for 1257006
> units...done
>
> 20100923 13:25:57| Computing probe affinities...done
>
> 20100923 13:25:57|Background correcting data set...done
>
> Could anyone please enlighten me with the type of the error? I will be
> highly obliged if anyone please help me with this problem.
>
> Thank you.
>
> Prithish Banerjee.
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
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Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Henrik Bengtsson
Hi,

sorry, my mistake.  I missed that you already did this.

You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
You can download it from Affymetrix and you'll find a link to their
support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
.  Download it (something like "MoEx-1_0-st-v1 Probe Sequences,
tabular format (130 MB, 3/19/08)") and place it in
annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is
correct by trying the following:

> library("aroma.affymetrix");
> ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
> ptf
AffymetrixProbeTabFile:
Name: MoEx-1_0-st-v1
Tags:
Full name: MoEx-1_0-st-v1
Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab
File size: 460.47 MB (482839635 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1.cdf
Filesize: 274.30MB
Chip type: MoEx-1_0-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1257006
Cells per unit: 5.21
Number of QC units: 0

If you get that to work, then your script should work.

Let me now if this solved your problem.

/Henrik

On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee
<[hidden email]> wrote:

> Respected Dr Bengtsson,
> My codes and outputs are as follows:
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.cn")
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data"
>> chipType <- "MoEx-1_0-st-v1"
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/MoEx-1_0-st-v1
> Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
> Filesize: 30.53MB
> Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 17831
> Cells per unit: 367.54
> Number of QC units: 1
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> print(csR)
> AffymetrixCelSet:
> Name: Exon Data
> Tags:
> Path: rawData/Exon Data/MoEx-1_0-st-v1
> Platform: Affymetrix
> Chip type: MoEx-1_0-st-v1
> Number of arrays: 7
> Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
> P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
> Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
> Total file size: 440.55MB
> RAM: 0.01MB
>> cdf <- getCdf(csR)
>> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>> setCdf(csR, cdfS)
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> print(bc)
> GcRmaBackgroundCorrection:
> Data set: Exon Data
> Input tags:
> User tags: *
> Asterisk ('*') tags: GRBC
> Output tags: GRBC
> Number of files: 7 (440.55MB)
> Platform: Affymetrix
> Chip type: MoEx-1_0-st-v1
> Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
> indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
> opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
> Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
> Is done: FALSE
> RAM: 0.00MB
>> csB <- process(bc, verbose=verbose)
> 20100927 16:31:40|Background correcting data set...
> 20100927 16:31:40| Computing probe affinities...
> 20100927 16:31:40|  Computing GCRMA probe affinities for 1257006 units...
> 20100927 16:31:40|   Identify PMs and MMs among the CDF cell indices...
>      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>        Mode   FALSE    TRUE    NA's
>     logical  334476 4931683       0
> 20100927 16:33:30|    MMs are defined as non-PMs
> 20100927 16:33:30|    Number of PMs: 4931683
> 20100927 16:33:30|    Number of MMs: 334476
> 20100927 16:33:30|   Identify PMs and MMs among the CDF cell indices...done
> 20100927 16:33:30|   Reading probe-sequence data...
> 20100927 16:33:30|    Retrieving probe-sequence data...
> 20100927 16:33:30|     Chip type (full): MoEx-1_0-st-v1
> 20100927 16:33:30|     Locating probe-tab file...
> 20100927 16:33:30|      Chip type: MoEx-1_0-st-v1
> Error in list(`process(bc, verbose = verbose)` = <environment>,
> `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = <environment>,
>  :
>
> [2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
> deprectated (v1) search rules:
>   at throw(Exception(...))
>   at throw.default("Found probe-tab file only by means of deprectated (v1
>   at throw("Found probe-tab file only by means of deprectated (v1) search
>   at method(static, ...)
>   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>   at method(static, ...)
>   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
>   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
>   at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
>   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
>   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>   at do.call("bgAdjustGcrma", args = args)
>   at process.GcRmaBackgroundCorrection(
> 20100927 16:33:30|     Locating probe-tab file...done
> 20100927 16:33:30|    Retrieving probe-sequence data...done
> 20100927 16:33:30|   Reading probe-sequence data...done
> 20100927 16:33:30|  Computing GCRMA probe affinities for 1257006
> units...done
> 20100927 16:33:30| Computing probe affinities...done
> 20100927 16:33:30|Background correcting data set...done
>> traceback()
> 17: throw.Exception(Exception(...))
> 16: throw(Exception(...))
> 15: throw.default("Found probe-tab file only by means of deprectated (v1)
> search rules: ",
>         pathname)
> 14: throw("Found probe-tab file only by means of deprectated (v1) search
> rules: ",
>         pathname)
> 13: method(static, ...)
> 12: AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>         ...)
> 11: method(static, ...)
> 10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
> less(verbose,
>         100))
> 9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
> verbose)
> 8: getProbeSequenceData(this, safe = safe, verbose = verbose)
> 7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>        verbose = less(verbose))
> 6: computeAffinities(cdf, paths = probePath, ..., verbose = less(verbose))
> 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 3: do.call("bgAdjustGcrma", args = args)
> 2: process.GcRmaBackgroundCorrection(bc, verbose = verbose)
> 1: process(bc, verbose = verbose)
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
>  [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7        affxparser_1.20.0
>  [4] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>  [7] matrixStats_0.2.1      R.rsp_0.4.0            R.filesets_0.9.0
> [10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.2
> [13] R.oo_1.7.4             R.methodsS3_1.2.1
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
> The working directory is desktop and the path for the cdf file and the raw
> data is as follows:
> /Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
> ( I have several other cdf files
> like MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
> and MoEx-1_0-st-v1.cdf in the same directory.)
> /Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/
> DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P2_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P3_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P6_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P14_(MoEx-1_0-st-v1).CEL
> Moreover I am following the thread and implementing the code you suggested
> there but it is not working with my dataset. Please help.
> Thank you,
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> first of all, for this chip type you need to specify:
>>
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>>
>> Moreover, you cannot use the custom CDF in the
>> GcRmaBackgroundCorrection step, and have to do the follow workaround
>> illustrated in the below example:
>>
>>
>> library("aroma.affymetrix");
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Affymetrix-Tissues";
>> chipType <- "MoEx-1_0-st-v1";
>>
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> # Setup data set
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR");
>> print(cdf);
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
>> print(csR);
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> # gcRMA-style background correction
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> # Currently, you must use the standard CDF file.
>> cdf <- getCdf(csR);
>> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
>> setCdf(csR, cdfS);
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> print(bc);
>> csB <- process(bc, verbose=verbose);
>> print(csB);
>> # Now, use the custom CDF in what follows
>> setCdf(csB, cdf);
>> print(csB);
>>
>> Yes, those last steps are rather confusing - we're working on updating
>> the code so you don't have to do that yourself.
>>
>> FYI, the above solution/workaround was resolved in thread 'GCRMA
>> normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
>> http://goo.gl/cniq.
>>
>> Hope this helps
>>
>> /Henrik
>>
>> On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
>> <[hidden email]> wrote:
>> > Hi All,
>> > I am trying to normalize a mouse exon array dataset using GCRMA
>> > normalization technique. I have exactly followed all the necessary steps
>> > for
>> > storing the dataset and the cdf file. the code and the output I am using
>> > are
>> > as follows:
>> >
>> > source("http://aroma-project.org/hbLite.R");
>> >
>> > hbInstall("aroma.affymetrix")
>> >
>> > source("http://aroma-project.org/hbLite.R");
>> >
>> > hbInstall("aroma.cn")
>> >
>> > verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >
>> > dataSet <- "Exon Data" [the path in the working directory is
>> > rawData/Exon
>> > Data/MoEx-1_0-st-v1/*.CEL files]
>> >
>> > chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
>> >
>> > annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>> >
>> > cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> > [converted to binary using convertCdf command]
>> >
>> > print(cdf)
>> >
>> > AffymetrixCdfFile:
>> >
>> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> >
>> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> >
>> > Filesize: 30.53MB
>> >
>> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> >
>> > RAM: 0.00MB
>> >
>> > File format: v4 (binary; XDA)
>> >
>> > Dimension: 2560x2560
>> >
>> > Number of cells: 6553600
>> >
>> > Number of units: 17831
>> >
>> > Cells per unit: 367.54
>> >
>> > Number of QC units: 1
>> >
>> > csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >
>> > print(csR)
>> >
>> > AffymetrixCelSet:
>> >
>> > Name: Exon Data
>> >
>> > Tags:
>> >
>> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> >
>> > Platform: Affymetrix
>> >
>> > Chip type: MoEx-1_0-st-v1
>> >
>> > Number of arrays: 7
>> >
>> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> >
>> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> >
>> > Total file size: 440.55MB
>> >
>> > RAM: 0.01MB
>> >
>> > cdf <- getCdf(csR)
>> >
>> > cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>> >
>> > setCdf(csR, cdfS)
>> >
>> > bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >
>> > print(bc)
>> >
>> > GcRmaBackgroundCorrection:
>> >
>> > Data set: Exon Data
>> >
>> > Input tags:
>> >
>> > User tags: *
>> >
>> > Asterisk ('*') tags: GRBC
>> >
>> > Output tags: GRBC
>> >
>> > Number of files: 7 (440.55MB)
>> >
>> > Platform: Affymetrix
>> >
>> > Chip type: MoEx-1_0-st-v1
>> >
>> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
>> > indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
>> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>> >
>> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> >
>> > Is done: FALSE
>> >
>> > RAM: 0.00MB
>> >
>> > csB <- process(bc, verbose=verbose)
>> >
>> > 20100923 13:24:12|Background correcting data set...
>> >
>> > 20100923 13:24:12| Computing probe affinities...
>> >
>> > 20100923 13:24:12|  Computing GCRMA probe affinities for 1257006
>> > units...
>> >
>> > 20100923 13:24:12|   Identify PMs and MMs among the CDF cell indices...
>> >
>> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >
>> >        Mode   FALSE    TRUE    NA's
>> >
>> >     logical  334476 4931683       0
>> >
>> > 20100923 13:25:57|    MMs are defined as non-PMs
>> >
>> > 20100923 13:25:57|    Number of PMs: 4931683
>> >
>> > 20100923 13:25:57|    Number of MMs: 334476
>> >
>> > 20100923 13:25:57|   Identify PMs and MMs among the CDF cell
>> > indices...done
>> >
>> > 20100923 13:25:57|   Reading probe-sequence data...
>> >
>> > 20100923 13:25:57|    Retrieving probe-sequence data...
>> >
>> > 20100923 13:25:57|     Chip type (full): MoEx-1_0-st-v1
>> >
>> > 20100923 13:25:57|     Locating probe-tab file...
>> >
>> > 20100923 13:25:57|      Chip type: MoEx-1_0-st-v1
>> >
>> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> > <environment>,
>> >  :
>> >
>> >
>> >
>> > [2010-09-23 13:25:57] Exception: Found probe-tab file only by means of
>> > deprectated (v1) search rules:
>> >
>> >   at throw(Exception(...))
>> >
>> >   at throw.default("Found probe-tab file only by means of deprectated
>> > (v1
>> >
>> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> > search
>> >
>> >   at method(static, ...)
>> >
>> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>> >
>> >   at method(static, ...)
>> >
>> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> > les
>> >
>> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>> >
>> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >
>> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> > ver
>> >
>> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> > less(verbos
>> >
>> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> > Data,GRBC/
>> >
>> >   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>> >
>> >   at do.call("bgAdjustGcrma", args = args)
>> >
>> >   at process.GcRmaBackgroundCorrection(
>> >
>> > 20100923 13:25:57|     Locating probe-tab file...done
>> >
>> > 20100923 13:25:57|    Retrieving probe-sequence data...done
>> >
>> > 20100923 13:25:57|   Reading probe-sequence data...done
>> >
>> > 20100923 13:25:57|  Computing GCRMA probe affinities for 1257006
>> > units...done
>> >
>> > 20100923 13:25:57| Computing probe affinities...done
>> >
>> > 20100923 13:25:57|Background correcting data set...done
>> >
>> > Could anyone please enlighten me with the type of the error? I will be
>> > highly obliged if anyone please help me with this problem.
>> >
>> > Thank you.
>> >
>> > Prithish Banerjee.
>> >
>> >
>> >
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to [hidden email]
>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
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Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Prithish Banerjee
Respected Dr Bengtsson,

Thank you for the help. I have done what you have suggested and the following output is as follows:

source("http://aroma-project.org/hbLite.R");

hbInstall("aroma.affymetrix")

source("http://aroma-project.org/hbLite.R");

hbInstall("aroma.cn")

verbose <- Arguments$getVerbose(-10, timestamp=TRUE); 

dataSet <- "Exon Data"

chipType <- "MoEx-1_0-st-v1"

cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")

print(cdf)

ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");

print(ptf)

csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)

print(csR)

cdf <- getCdf(csR)

cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))

setCdf(csR, cdfS)

bc <- GcRmaBackgroundCorrection(csR, type="affinities")

print(bc)

csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
20100928 22:40:59|Background correcting data set...
20100928 22:41:09| Computing probe affinities...
20100928 22:41:09|  Reading saved affinities: probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...
20100928 22:41:10|  Reading saved affinities: probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...done
20100928 22:41:10|  RAM: 50.00MB
20100928 22:41:10| Computing probe affinities...done
20100928 22:41:10| Background correcting data set...
20100928 22:41:16|  Already background corrected for "optical" effects
20100928 22:41:16| Background correcting data set...done
20100928 22:41:16| Estimating specific binding parameters...
20100928 22:41:16|  Extracting PM indices...
20100928 22:41:16|   Reading cell indices from CDF file...
20100928 22:41:16|    Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf
20100928 22:41:16|    Units: 
     NULL
20100928 22:41:16|    lapplyInChunks()...
20100928 22:41:16|     Number of elements per chunk: 1e+05
20100928 22:41:16|     Chunk #1 of 13...
20100928 22:41:16|      Elements: 
       int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
20100928 22:41:16|      Querying CDF file...
20100928 22:41:20|      Querying CDF file...done
20100928 22:41:21|      Restructuring...
20100928 22:41:21|      Restructuring...done
                 used (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058626  110    6907341 368.9  17756025 948.3
      Vcells 14800385  113   55506200 423.5 106800686 814.9
20100928 22:41:21|     Chunk #1 of 13...done
20100928 22:41:21|     Chunk #2 of 13...
20100928 22:41:21|      Elements: 
       int [1:100000] 100001 100002 100003 100004 100005 100006 100007 100008 100009 100010 ...
20100928 22:41:21|      Querying CDF file...
20100928 22:41:25|      Querying CDF file...done
20100928 22:41:26|      Restructuring...
20100928 22:41:26|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058632 110.0    6907341 368.9  17756025 948.3
      Vcells 14946933 114.1   44404960 338.8 106800686 814.9
20100928 22:41:26|     Chunk #2 of 13...done
20100928 22:41:26|     Chunk #3 of 13...
20100928 22:41:26|      Elements: 
       int [1:100000] 200001 200002 200003 200004 200005 200006 200007 200008 200009 200010 ...
20100928 22:41:26|      Querying CDF file...
20100928 22:41:30|      Querying CDF file...done
20100928 22:41:30|      Restructuring...
20100928 22:41:30|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058634 110.0    6907341 368.9  17756025 948.3
      Vcells 15101344 115.3   44404960 338.8 106800686 814.9
20100928 22:41:31|     Chunk #3 of 13...done
20100928 22:41:31|     Chunk #4 of 13...
20100928 22:41:31|      Elements: 
       int [1:100000] 300001 300002 300003 300004 300005 300006 300007 300008 300009 300010 ...
20100928 22:41:31|      Querying CDF file...
20100928 22:41:35|      Querying CDF file...done
20100928 22:41:35|      Restructuring...
20100928 22:41:35|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058634 110.0    6907341 368.9  17756025 948.3
      Vcells 15249056 116.4   44404960 338.8 106800686 814.9
20100928 22:41:36|     Chunk #4 of 13...done
20100928 22:41:36|     Chunk #5 of 13...
20100928 22:41:36|      Elements: 
       int [1:100000] 400001 400002 400003 400004 400005 400006 400007 400008 400009 400010 ...
20100928 22:41:36|      Querying CDF file...
20100928 22:41:40|      Querying CDF file...done
20100928 22:41:40|      Restructuring...
20100928 22:41:40|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058635 110.0    6907341 368.9  17756025 948.3
      Vcells 15397125 117.5   44404960 338.8 106800686 814.9
20100928 22:41:40|     Chunk #5 of 13...done
20100928 22:41:40|     Chunk #6 of 13...
20100928 22:41:40|      Elements: 
       int [1:100000] 500001 500002 500003 500004 500005 500006 500007 500008 500009 500010 ...
20100928 22:41:40|      Querying CDF file...
20100928 22:41:44|      Querying CDF file...done
20100928 22:41:45|      Restructuring...
20100928 22:41:45|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058637 110.0    6907341 368.9  17756025 948.3
      Vcells 15541779 118.6   44404960 338.8 106800686 814.9
20100928 22:41:45|     Chunk #6 of 13...done
20100928 22:41:45|     Chunk #7 of 13...
20100928 22:41:45|      Elements: 
       int [1:100000] 600001 600002 600003 600004 600005 600006 600007 600008 600009 600010 ...
20100928 22:41:45|      Querying CDF file...
20100928 22:41:49|      Querying CDF file...done
20100928 22:41:50|      Restructuring...
20100928 22:41:50|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058637 110.0    6907341 368.9  17756025 948.3
      Vcells 15690489 119.8   44404960 338.8 106800686 814.9
20100928 22:41:50|     Chunk #7 of 13...done
20100928 22:41:50|     Chunk #8 of 13...
20100928 22:41:50|      Elements: 
       int [1:100000] 700001 700002 700003 700004 700005 700006 700007 700008 700009 700010 ...
20100928 22:41:50|      Querying CDF file...
20100928 22:41:54|      Querying CDF file...done
20100928 22:41:54|      Restructuring...
20100928 22:41:54|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058638 110.0    6907341 368.9  17756025 948.3
      Vcells 15837280 120.9   44404960 338.8 106800686 814.9
20100928 22:41:55|     Chunk #8 of 13...done
20100928 22:41:55|     Chunk #9 of 13...
20100928 22:41:55|      Elements: 
       int [1:100000] 800001 800002 800003 800004 800005 800006 800007 800008 800009 800010 ...
20100928 22:41:55|      Querying CDF file...
20100928 22:41:59|      Querying CDF file...done
20100928 22:41:59|      Restructuring...
20100928 22:41:59|      Restructuring...done
                 used (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058640  110    6907341 368.9  17756025 948.3
      Vcells 15987604  122   44404960 338.8 106800686 814.9
20100928 22:41:59|     Chunk #9 of 13...done
20100928 22:41:59|     Chunk #10 of 13...
20100928 22:41:59|      Elements: 
       int [1:100000] 900001 900002 900003 900004 900005 900006 900007 900008 900009 900010 ...
20100928 22:41:59|      Querying CDF file...
20100928 22:42:04|      Querying CDF file...done
20100928 22:42:04|      Restructuring...
20100928 22:42:04|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2066219 110.4    6907341 368.9  17756025 948.3
      Vcells 16292565 124.4   44404960 338.8 106800686 814.9
20100928 22:42:04|     Chunk #10 of 13...done
20100928 22:42:04|     Chunk #11 of 13...
20100928 22:42:04|      Elements: 
       int [1:100000] 1000001 1000002 1000003 1000004 1000005 1000006 1000007 1000008 1000009 1000010 ...
20100928 22:42:05|      Querying CDF file...
20100928 22:42:08|      Querying CDF file...done
20100928 22:42:09|      Restructuring...
20100928 22:42:09|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058641 110.0    6907341 368.9  17756025 948.3
      Vcells 16431821 125.4   44404960 338.8 106800686 814.9
20100928 22:42:09|     Chunk #11 of 13...done
20100928 22:42:09|     Chunk #12 of 13...
20100928 22:42:09|      Elements: 
       int [1:100000] 1100001 1100002 1100003 1100004 1100005 1100006 1100007 1100008 1100009 1100010 ...
20100928 22:42:09|      Querying CDF file...
20100928 22:42:13|      Querying CDF file...done
20100928 22:42:14|      Restructuring...
20100928 22:42:14|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  2058642 110.0    6907341 368.9  17756025 948.3
      Vcells 16577525 126.5   44404960 338.8 106800686 814.9
20100928 22:42:14|     Chunk #12 of 13...done
20100928 22:42:14|     Chunk #13 of 13...
20100928 22:42:14|      Elements: 
       int [1:57006] 1200001 1200002 1200003 1200004 1200005 1200006 1200007 1200008 1200009 1200010 ...
20100928 22:42:14|      Querying CDF file...
20100928 22:42:16|      Querying CDF file...done
20100928 22:42:17|      Restructuring...
20100928 22:42:17|      Restructuring...done
                 used  (Mb) gc trigger  (Mb)  max used  (Mb)
      Ncells  1671697  89.3    5525872 295.2  17756025 948.3
      Vcells 16271204 124.2   44404960 338.8 106800686 814.9
20100928 22:42:17|     Chunk #13 of 13...done
20100928 22:42:17|    lapplyInChunks()...done
20100928 22:42:17|   Reading cell indices from CDF file...done
              used  (Mb) gc trigger  (Mb)  max used  (Mb)
   Ncells  1158492  61.9    4420697 236.1  17756025 948.3
   Vcells 13870500 105.9   44404960 338.8 106800686 814.9
20100928 22:42:17|   readUnits.AffymetrixCdfFile(): Updating cache
20100928 22:43:21|  Extracting PM indices...done
             used (Mb) gc trigger  (Mb)  max used  (Mb)
  Ncells  1158442 61.9    6163167 329.2  17756025 948.3
  Vcells 11250131 85.9   35523968 271.1 106800686 814.9
20100928 22:43:22|  Extracting 25000 random PM intensities across CEL set...
20100928 22:43:22|   Array #1 of 7...
20100928 22:43:22|   Array #1 of 7...done
20100928 22:43:22|   Array #2 of 7...
20100928 22:43:23|   Array #2 of 7...done
20100928 22:43:23|   Array #3 of 7...
20100928 22:43:24|   Array #3 of 7...done
20100928 22:43:24|   Array #4 of 7...
20100928 22:43:26|   Array #4 of 7...done
20100928 22:43:26|   Array #5 of 7...
20100928 22:43:27|   Array #5 of 7...done
20100928 22:43:27|   Array #6 of 7...
20100928 22:43:28|   Array #6 of 7...done
20100928 22:43:28|   Array #7 of 7...
20100928 22:43:30|   Array #7 of 7...done
              used (Mb) gc trigger  (Mb)  max used  (Mb)
   Ncells  1158299 61.9    4930533 263.4  17756025 948.3
   Vcells 11274772 86.1   35523968 271.1 106800686 814.9
20100928 22:43:31|  Extracting 25000 random PM intensities across CEL set...done
20100928 22:43:31|  Extracting probe affinities and fitting linear model...
              used (Mb) gc trigger  (Mb)  max used  (Mb)
   Ncells  1158298 61.9    3944426 210.7  17756025 948.3
   Vcells 11287264 86.2   35523968 271.1 106800686 814.9
20100928 22:43:32|   Fitting the GCRMA background linear model...
     num [1:25000] 5.39 8.46 8.41 6.89 8.05 ...
     num [1:25000] 0.485 -0.764 1.766 -0.857 0.344 ...
    
    Call:
    lm(formula = pm.random2 ~ aff)
    
    Coefficients:
    (Intercept)          aff  
         6.5646       0.4193  
    
20100928 22:43:32|   Fitting the GCRMA background linear model...done
20100928 22:43:32|  Extracting probe affinities and fitting linear model...done
20100928 22:43:32| Estimating specific binding parameters...done
20100928 22:43:32| Adjusting 7 arrays...
20100928 22:43:32|  Array #1 of 7...
   AffymetrixCelFile:
   Name: DK Litter D15 P1_(MoEx-1_0-st-v1)
   Tags: 
   Full name: DK Litter D15 P1_(MoEx-1_0-st-v1)
   Pathname: probeData/Exon Data,OBC/MoEx-1_0-st-v1/DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
   File size: 62.50 MB (65536703 bytes)
   RAM: 0.00 MB
   File format: v4 (binary; XDA)
   Platform: Affymetrix
   Chip type: MoEx-1_0-st-v1
   Timestamp: 2010-09-28 14:26:37
20100928 22:43:32|   Obtaining PM and MM signals and affinities...
20100928 22:45:16|   Obtaining PM and MM signals and affinities...done
20100928 22:45:16|   Estimating non-specific binding parameters...
Error in quantile.default(a1, 0.001) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE
20100928 22:45:16|  Array #1 of 7...done
20100928 22:45:16| Adjusting 7 arrays...done
20100928 22:45:16|Background correcting data set...done
> traceback()
15: stop("missing values and NaN's not allowed if 'na.rm' is FALSE")
14: quantile.default(a1, 0.001)
13: quantile(a1, 0.001)
12: seq(quantile(a1, 0.001), quantile(a1, 0.999), len = 26)
11: cut.default(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1, 
        0.999), len = 26), Inf))
10: cut(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1, 0.999), 
        len = 26), Inf))
9: bg.parameters.ns(ncs[index.affinities], anc, apm)
8: gcrma::bg.adjust.affinities(pm, mm, apm, amm, index.affinities = 1:length(pm), 
       k = k, fast = fast)
7: bgAdjustGcrma.AffymetrixCelFile(df, path = path, type = type, 
       indicesNegativeControl = indicesNegativeControl, affinities = affinities, 
       gsbAdjust = gsbAdjust, parametersGsb = parametersGsb, k = k, 
       rho = rho, stretch = stretch, fast = fast, overwrite = overwrite, 
       skip = skip, ..., verbose = less(verbose), .deprecated = .deprecated)
6: bgAdjustGcrma(df, path = path, type = type, indicesNegativeControl = indicesNegativeControl, 
       affinities = affinities, gsbAdjust = gsbAdjust, parametersGsb = parametersGsb, 
       k = k, rho = rho, stretch = stretch, fast = fast, overwrite = overwrite, 
       skip = skip, ..., verbose = less(verbose), .deprecated = .deprecated)
5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1", 
       verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL, 
       typesToUpdate = "pm", indicesNegativeControl = NULL, affinities = NULL, 
       type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE, 
       gsbParameters = NULL, .deprecated = FALSE)
4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1", 
       verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL, 
       typesToUpdate = "pm", indicesNegativeControl = NULL, affinities = NULL, 
       type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE, 
       gsbParameters = NULL, .deprecated = FALSE)
3: do.call("bgAdjustGcrma", args = args)
2: process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose = verbose, 
       na.rm = "TRUE")
1: process(bc, cdf = cdf, ptf = ptf, verbose = verbose)


Is it somehow  possible to replace the NaN and missing values to some other value (like the mean or median or some small number close to 0)?
Also I am getting some output in the probeData folder as:
probeData/Exon Data,OBC/MoEx-1_0-st-v1/(all the *.cel files) and probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa.
What are this outputs corresponds to?

Again thank you for the help.

Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.


On Tue, Sep 28, 2010 at 1:47 AM, Henrik Bengtsson <[hidden email]> wrote:
Hi,

sorry, my mistake.  I missed that you already did this.

You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
You can download it from Affymetrix and you'll find a link to their
support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
.  Download it (something like "MoEx-1_0-st-v1 Probe Sequences,
tabular format (130 MB, 3/19/08)") and place it in
annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is
correct by trying the following:

> library("aroma.affymetrix");
> ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
> ptf
AffymetrixProbeTabFile:
Name: MoEx-1_0-st-v1
Tags:
Full name: MoEx-1_0-st-v1
Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab
File size: 460.47 MB (482839635 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1.cdf
Filesize: 274.30MB
Chip type: MoEx-1_0-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1257006
Cells per unit: 5.21
Number of QC units: 0

If you get that to work, then your script should work.

Let me now if this solved your problem.

/Henrik

On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee
<[hidden email]> wrote:
> Respected Dr Bengtsson,
> My codes and outputs are as follows:
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.cn")
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data"
>> chipType <- "MoEx-1_0-st-v1"
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/MoEx-1_0-st-v1
> Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
> Filesize: 30.53MB
> Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 17831
> Cells per unit: 367.54
> Number of QC units: 1
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> print(csR)
> AffymetrixCelSet:
> Name: Exon Data
> Tags:
> Path: rawData/Exon Data/MoEx-1_0-st-v1
> Platform: Affymetrix
> Chip type: MoEx-1_0-st-v1
> Number of arrays: 7
> Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
> P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
> Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
> Total file size: 440.55MB
> RAM: 0.01MB
>> cdf <- getCdf(csR)
>> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>> setCdf(csR, cdfS)
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> print(bc)
> GcRmaBackgroundCorrection:
> Data set: Exon Data
> Input tags:
> User tags: *
> Asterisk ('*') tags: GRBC
> Output tags: GRBC
> Number of files: 7 (440.55MB)
> Platform: Affymetrix
> Chip type: MoEx-1_0-st-v1
> Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
> indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
> opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
> Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
> Is done: FALSE
> RAM: 0.00MB
>> csB <- process(bc, verbose=verbose)
> 20100927 16:31:40|Background correcting data set...
> 20100927 16:31:40| Computing probe affinities...
> 20100927 16:31:40|  Computing GCRMA probe affinities for 1257006 units...
> 20100927 16:31:40|   Identify PMs and MMs among the CDF cell indices...
>      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>        Mode   FALSE    TRUE    NA's
>     logical  334476 4931683       0
> 20100927 16:33:30|    MMs are defined as non-PMs
> 20100927 16:33:30|    Number of PMs: 4931683
> 20100927 16:33:30|    Number of MMs: 334476
> 20100927 16:33:30|   Identify PMs and MMs among the CDF cell indices...done
> 20100927 16:33:30|   Reading probe-sequence data...
> 20100927 16:33:30|    Retrieving probe-sequence data...
> 20100927 16:33:30|     Chip type (full): MoEx-1_0-st-v1
> 20100927 16:33:30|     Locating probe-tab file...
> 20100927 16:33:30|      Chip type: MoEx-1_0-st-v1
> Error in list(`process(bc, verbose = verbose)` = <environment>,
> `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = <environment>,
>  :
>
> [2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
> deprectated (v1) search rules:
>   at throw(Exception(...))
>   at throw.default("Found probe-tab file only by means of deprectated (v1
>   at throw("Found probe-tab file only by means of deprectated (v1) search
>   at method(static, ...)
>   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>   at method(static, ...)
>   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
>   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
>   at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
>   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
>   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>   at do.call("bgAdjustGcrma", args = args)
>   at process.GcRmaBackgroundCorrection(
> 20100927 16:33:30|     Locating probe-tab file...done
> 20100927 16:33:30|    Retrieving probe-sequence data...done
> 20100927 16:33:30|   Reading probe-sequence data...done
> 20100927 16:33:30|  Computing GCRMA probe affinities for 1257006
> units...done
> 20100927 16:33:30| Computing probe affinities...done
> 20100927 16:33:30|Background correcting data set...done
>> traceback()
> 17: throw.Exception(Exception(...))
> 16: throw(Exception(...))
> 15: throw.default("Found probe-tab file only by means of deprectated (v1)
> search rules: ",
>         pathname)
> 14: throw("Found probe-tab file only by means of deprectated (v1) search
> rules: ",
>         pathname)
> 13: method(static, ...)
> 12: AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>         ...)
> 11: method(static, ...)
> 10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
> less(verbose,
>         100))
> 9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
> verbose)
> 8: getProbeSequenceData(this, safe = safe, verbose = verbose)
> 7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>        verbose = less(verbose))
> 6: computeAffinities(cdf, paths = probePath, ..., verbose = less(verbose))
> 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 3: do.call("bgAdjustGcrma", args = args)
> 2: process.GcRmaBackgroundCorrection(bc, verbose = verbose)
> 1: process(bc, verbose = verbose)
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
>  [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7        affxparser_1.20.0
>  [4] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>  [7] matrixStats_0.2.1      R.rsp_0.4.0            R.filesets_0.9.0
> [10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.2
> [13] R.oo_1.7.4             R.methodsS3_1.2.1
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
> The working directory is desktop and the path for the cdf file and the raw
> data is as follows:
> /Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
> ( I have several other cdf files
> like MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
> and MoEx-1_0-st-v1.cdf in the same directory.)
> /Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/
> DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P2_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P3_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P6_(MoEx-1_0-st-v1).CEL
> DK Litter D15 P14_(MoEx-1_0-st-v1).CEL
> Moreover I am following the thread and implementing the code you suggested
> there but it is not working with my dataset. Please help.
> Thank you,
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> first of all, for this chip type you need to specify:
>>
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>>
>> Moreover, you cannot use the custom CDF in the
>> GcRmaBackgroundCorrection step, and have to do the follow workaround
>> illustrated in the below example:
>>
>>
>> library("aroma.affymetrix");
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Affymetrix-Tissues";
>> chipType <- "MoEx-1_0-st-v1";
>>
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> # Setup data set
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR");
>> print(cdf);
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
>> print(csR);
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> # gcRMA-style background correction
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> # Currently, you must use the standard CDF file.
>> cdf <- getCdf(csR);
>> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
>> setCdf(csR, cdfS);
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> print(bc);
>> csB <- process(bc, verbose=verbose);
>> print(csB);
>> # Now, use the custom CDF in what follows
>> setCdf(csB, cdf);
>> print(csB);
>>
>> Yes, those last steps are rather confusing - we're working on updating
>> the code so you don't have to do that yourself.
>>
>> FYI, the above solution/workaround was resolved in thread 'GCRMA
>> normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
>> http://goo.gl/cniq.
>>
>> Hope this helps
>>
>> /Henrik
>>
>> On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
>> <[hidden email]> wrote:
>> > Hi All,
>> > I am trying to normalize a mouse exon array dataset using GCRMA
>> > normalization technique. I have exactly followed all the necessary steps
>> > for
>> > storing the dataset and the cdf file. the code and the output I am using
>> > are
>> > as follows:
>> >
>> > source("http://aroma-project.org/hbLite.R");
>> >
>> > hbInstall("aroma.affymetrix")
>> >
>> > source("http://aroma-project.org/hbLite.R");
>> >
>> > hbInstall("aroma.cn")
>> >
>> > verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >
>> > dataSet <- "Exon Data" [the path in the working directory is
>> > rawData/Exon
>> > Data/MoEx-1_0-st-v1/*.CEL files]
>> >
>> > chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
>> >
>> > annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>> >
>> > cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> > [converted to binary using convertCdf command]
>> >
>> > print(cdf)
>> >
>> > AffymetrixCdfFile:
>> >
>> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> >
>> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> >
>> > Filesize: 30.53MB
>> >
>> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> >
>> > RAM: 0.00MB
>> >
>> > File format: v4 (binary; XDA)
>> >
>> > Dimension: 2560x2560
>> >
>> > Number of cells: 6553600
>> >
>> > Number of units: 17831
>> >
>> > Cells per unit: 367.54
>> >
>> > Number of QC units: 1
>> >
>> > csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >
>> > print(csR)
>> >
>> > AffymetrixCelSet:
>> >
>> > Name: Exon Data
>> >
>> > Tags:
>> >
>> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> >
>> > Platform: Affymetrix
>> >
>> > Chip type: MoEx-1_0-st-v1
>> >
>> > Number of arrays: 7
>> >
>> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> >
>> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> >
>> > Total file size: 440.55MB
>> >
>> > RAM: 0.01MB
>> >
>> > cdf <- getCdf(csR)
>> >
>> > cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>> >
>> > setCdf(csR, cdfS)
>> >
>> > bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >
>> > print(bc)
>> >
>> > GcRmaBackgroundCorrection:
>> >
>> > Data set: Exon Data
>> >
>> > Input tags:
>> >
>> > User tags: *
>> >
>> > Asterisk ('*') tags: GRBC
>> >
>> > Output tags: GRBC
>> >
>> > Number of files: 7 (440.55MB)
>> >
>> > Platform: Affymetrix
>> >
>> > Chip type: MoEx-1_0-st-v1
>> >
>> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
>> > indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
>> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>> >
>> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> >
>> > Is done: FALSE
>> >
>> > RAM: 0.00MB
>> >
>> > csB <- process(bc, verbose=verbose)
>> >
>> > 20100923 13:24:12|Background correcting data set...
>> >
>> > 20100923 13:24:12| Computing probe affinities...
>> >
>> > 20100923 13:24:12|  Computing GCRMA probe affinities for 1257006
>> > units...
>> >
>> > 20100923 13:24:12|   Identify PMs and MMs among the CDF cell indices...
>> >
>> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >
>> >        Mode   FALSE    TRUE    NA's
>> >
>> >     logical  334476 4931683       0
>> >
>> > 20100923 13:25:57|    MMs are defined as non-PMs
>> >
>> > 20100923 13:25:57|    Number of PMs: 4931683
>> >
>> > 20100923 13:25:57|    Number of MMs: 334476
>> >
>> > 20100923 13:25:57|   Identify PMs and MMs among the CDF cell
>> > indices...done
>> >
>> > 20100923 13:25:57|   Reading probe-sequence data...
>> >
>> > 20100923 13:25:57|    Retrieving probe-sequence data...
>> >
>> > 20100923 13:25:57|     Chip type (full): MoEx-1_0-st-v1
>> >
>> > 20100923 13:25:57|     Locating probe-tab file...
>> >
>> > 20100923 13:25:57|      Chip type: MoEx-1_0-st-v1
>> >
>> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> > <environment>,
>> >  :
>> >
>> >
>> >
>> > [2010-09-23 13:25:57] Exception: Found probe-tab file only by means of
>> > deprectated (v1) search rules:
>> >
>> >   at throw(Exception(...))
>> >
>> >   at throw.default("Found probe-tab file only by means of deprectated
>> > (v1
>> >
>> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> > search
>> >
>> >   at method(static, ...)
>> >
>> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>> >
>> >   at method(static, ...)
>> >
>> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> > les
>> >
>> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>> >
>> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >
>> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> > ver
>> >
>> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> > less(verbos
>> >
>> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> > Data,GRBC/
>> >
>> >   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>> >
>> >   at do.call("bgAdjustGcrma", args = args)
>> >
>> >   at process.GcRmaBackgroundCorrection(
>> >
>> > 20100923 13:25:57|     Locating probe-tab file...done
>> >
>> > 20100923 13:25:57|    Retrieving probe-sequence data...done
>> >
>> > 20100923 13:25:57|   Reading probe-sequence data...done
>> >
>> > 20100923 13:25:57|  Computing GCRMA probe affinities for 1257006
>> > units...done
>> >
>> > 20100923 13:25:57| Computing probe affinities...done
>> >
>> > 20100923 13:25:57|Background correcting data set...done
>> >
>> > Could anyone please enlighten me with the type of the error? I will be
>> > highly obliged if anyone please help me with this problem.
>> >
>> > Thank you.
>> >
>> > Prithish Banerjee.
>> >
>> >
>> >
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to [hidden email]
>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
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Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Henrik Bengtsson
Hi.

On Wed, Sep 29, 2010 at 10:32 AM, Prithish Banerjee
<[hidden email]> wrote:

> Respected Dr Bengtsson,
> Thank you for the help. I have done what you have suggested and the
> following output is as follows:
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.affymetrix")
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.cn")
>
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>
> dataSet <- "Exon Data"
>
> chipType <- "MoEx-1_0-st-v1"
>
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>
> print(cdf)
>
> ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
>
> print(ptf)
>
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>
> print(csR)
>
> cdf <- getCdf(csR)
>
> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>
> setCdf(csR, cdfS)
>
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>
> print(bc)
>
> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
> 20100928 22:40:59|Background correcting data set...
> 20100928 22:41:09| Computing probe affinities...
> 20100928 22:41:09|  Reading saved affinities: probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...
> 20100928 22:41:10|  Reading saved affinities: probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...done
> 20100928 22:41:10|  RAM: 50.00MB
> 20100928 22:41:10| Computing probe affinities...done
> 20100928 22:41:10| Background correcting data set...
> 20100928 22:41:16|  Already background corrected for "optical" effects
> 20100928 22:41:16| Background correcting data set...done
> 20100928 22:41:16| Estimating specific binding parameters...
> 20100928 22:41:16|  Extracting PM indices...
> 20100928 22:41:16|   Reading cell indices from CDF file...
> 20100928 22:41:16|    Pathname:
> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf
> 20100928 22:41:16|    Units:
>      NULL
> 20100928 22:41:16|    lapplyInChunks()...
> 20100928 22:41:16|     Number of elements per chunk: 1e+05
> 20100928 22:41:16|     Chunk #1 of 13...
> 20100928 22:41:16|      Elements:
>        int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
> 20100928 22:41:16|      Querying CDF file...
> 20100928 22:41:20|      Querying CDF file...done
> 20100928 22:41:21|      Restructuring...
> 20100928 22:41:21|      Restructuring...done
>                  used (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058626  110    6907341 368.9  17756025 948.3
>       Vcells 14800385  113   55506200 423.5 106800686 814.9
> 20100928 22:41:21|     Chunk #1 of 13...done
> 20100928 22:41:21|     Chunk #2 of 13...
> 20100928 22:41:21|      Elements:
>        int [1:100000] 100001 100002 100003 100004 100005 100006 100007
> 100008 100009 100010 ...
> 20100928 22:41:21|      Querying CDF file...
> 20100928 22:41:25|      Querying CDF file...done
> 20100928 22:41:26|      Restructuring...
> 20100928 22:41:26|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058632 110.0    6907341 368.9  17756025 948.3
>       Vcells 14946933 114.1   44404960 338.8 106800686 814.9
> 20100928 22:41:26|     Chunk #2 of 13...done
> 20100928 22:41:26|     Chunk #3 of 13...
> 20100928 22:41:26|      Elements:
>        int [1:100000] 200001 200002 200003 200004 200005 200006 200007
> 200008 200009 200010 ...
> 20100928 22:41:26|      Querying CDF file...
> 20100928 22:41:30|      Querying CDF file...done
> 20100928 22:41:30|      Restructuring...
> 20100928 22:41:30|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058634 110.0    6907341 368.9  17756025 948.3
>       Vcells 15101344 115.3   44404960 338.8 106800686 814.9
> 20100928 22:41:31|     Chunk #3 of 13...done
> 20100928 22:41:31|     Chunk #4 of 13...
> 20100928 22:41:31|      Elements:
>        int [1:100000] 300001 300002 300003 300004 300005 300006 300007
> 300008 300009 300010 ...
> 20100928 22:41:31|      Querying CDF file...
> 20100928 22:41:35|      Querying CDF file...done
> 20100928 22:41:35|      Restructuring...
> 20100928 22:41:35|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058634 110.0    6907341 368.9  17756025 948.3
>       Vcells 15249056 116.4   44404960 338.8 106800686 814.9
> 20100928 22:41:36|     Chunk #4 of 13...done
> 20100928 22:41:36|     Chunk #5 of 13...
> 20100928 22:41:36|      Elements:
>        int [1:100000] 400001 400002 400003 400004 400005 400006 400007
> 400008 400009 400010 ...
> 20100928 22:41:36|      Querying CDF file...
> 20100928 22:41:40|      Querying CDF file...done
> 20100928 22:41:40|      Restructuring...
> 20100928 22:41:40|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058635 110.0    6907341 368.9  17756025 948.3
>       Vcells 15397125 117.5   44404960 338.8 106800686 814.9
> 20100928 22:41:40|     Chunk #5 of 13...done
> 20100928 22:41:40|     Chunk #6 of 13...
> 20100928 22:41:40|      Elements:
>        int [1:100000] 500001 500002 500003 500004 500005 500006 500007
> 500008 500009 500010 ...
> 20100928 22:41:40|      Querying CDF file...
> 20100928 22:41:44|      Querying CDF file...done
> 20100928 22:41:45|      Restructuring...
> 20100928 22:41:45|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058637 110.0    6907341 368.9  17756025 948.3
>       Vcells 15541779 118.6   44404960 338.8 106800686 814.9
> 20100928 22:41:45|     Chunk #6 of 13...done
> 20100928 22:41:45|     Chunk #7 of 13...
> 20100928 22:41:45|      Elements:
>        int [1:100000] 600001 600002 600003 600004 600005 600006 600007
> 600008 600009 600010 ...
> 20100928 22:41:45|      Querying CDF file...
> 20100928 22:41:49|      Querying CDF file...done
> 20100928 22:41:50|      Restructuring...
> 20100928 22:41:50|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058637 110.0    6907341 368.9  17756025 948.3
>       Vcells 15690489 119.8   44404960 338.8 106800686 814.9
> 20100928 22:41:50|     Chunk #7 of 13...done
> 20100928 22:41:50|     Chunk #8 of 13...
> 20100928 22:41:50|      Elements:
>        int [1:100000] 700001 700002 700003 700004 700005 700006 700007
> 700008 700009 700010 ...
> 20100928 22:41:50|      Querying CDF file...
> 20100928 22:41:54|      Querying CDF file...done
> 20100928 22:41:54|      Restructuring...
> 20100928 22:41:54|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058638 110.0    6907341 368.9  17756025 948.3
>       Vcells 15837280 120.9   44404960 338.8 106800686 814.9
> 20100928 22:41:55|     Chunk #8 of 13...done
> 20100928 22:41:55|     Chunk #9 of 13...
> 20100928 22:41:55|      Elements:
>        int [1:100000] 800001 800002 800003 800004 800005 800006 800007
> 800008 800009 800010 ...
> 20100928 22:41:55|      Querying CDF file...
> 20100928 22:41:59|      Querying CDF file...done
> 20100928 22:41:59|      Restructuring...
> 20100928 22:41:59|      Restructuring...done
>                  used (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058640  110    6907341 368.9  17756025 948.3
>       Vcells 15987604  122   44404960 338.8 106800686 814.9
> 20100928 22:41:59|     Chunk #9 of 13...done
> 20100928 22:41:59|     Chunk #10 of 13...
> 20100928 22:41:59|      Elements:
>        int [1:100000] 900001 900002 900003 900004 900005 900006 900007
> 900008 900009 900010 ...
> 20100928 22:41:59|      Querying CDF file...
> 20100928 22:42:04|      Querying CDF file...done
> 20100928 22:42:04|      Restructuring...
> 20100928 22:42:04|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2066219 110.4    6907341 368.9  17756025 948.3
>       Vcells 16292565 124.4   44404960 338.8 106800686 814.9
> 20100928 22:42:04|     Chunk #10 of 13...done
> 20100928 22:42:04|     Chunk #11 of 13...
> 20100928 22:42:04|      Elements:
>        int [1:100000] 1000001 1000002 1000003 1000004 1000005 1000006
> 1000007 1000008 1000009 1000010 ...
> 20100928 22:42:05|      Querying CDF file...
> 20100928 22:42:08|      Querying CDF file...done
> 20100928 22:42:09|      Restructuring...
> 20100928 22:42:09|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058641 110.0    6907341 368.9  17756025 948.3
>       Vcells 16431821 125.4   44404960 338.8 106800686 814.9
> 20100928 22:42:09|     Chunk #11 of 13...done
> 20100928 22:42:09|     Chunk #12 of 13...
> 20100928 22:42:09|      Elements:
>        int [1:100000] 1100001 1100002 1100003 1100004 1100005 1100006
> 1100007 1100008 1100009 1100010 ...
> 20100928 22:42:09|      Querying CDF file...
> 20100928 22:42:13|      Querying CDF file...done
> 20100928 22:42:14|      Restructuring...
> 20100928 22:42:14|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058642 110.0    6907341 368.9  17756025 948.3
>       Vcells 16577525 126.5   44404960 338.8 106800686 814.9
> 20100928 22:42:14|     Chunk #12 of 13...done
> 20100928 22:42:14|     Chunk #13 of 13...
> 20100928 22:42:14|      Elements:
>        int [1:57006] 1200001 1200002 1200003 1200004 1200005 1200006 1200007
> 1200008 1200009 1200010 ...
> 20100928 22:42:14|      Querying CDF file...
> 20100928 22:42:16|      Querying CDF file...done
> 20100928 22:42:17|      Restructuring...
> 20100928 22:42:17|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  1671697  89.3    5525872 295.2  17756025 948.3
>       Vcells 16271204 124.2   44404960 338.8 106800686 814.9
> 20100928 22:42:17|     Chunk #13 of 13...done
> 20100928 22:42:17|    lapplyInChunks()...done
> 20100928 22:42:17|   Reading cell indices from CDF file...done
>               used  (Mb) gc trigger  (Mb)  max used  (Mb)
>    Ncells  1158492  61.9    4420697 236.1  17756025 948.3
>    Vcells 13870500 105.9   44404960 338.8 106800686 814.9
> 20100928 22:42:17|   readUnits.AffymetrixCdfFile(): Updating cache
> 20100928 22:43:21|  Extracting PM indices...done
>              used (Mb) gc trigger  (Mb)  max used  (Mb)
>   Ncells  1158442 61.9    6163167 329.2  17756025 948.3
>   Vcells 11250131 85.9   35523968 271.1 106800686 814.9
> 20100928 22:43:22|  Extracting 25000 random PM intensities across CEL set...
> 20100928 22:43:22|   Array #1 of 7...
> 20100928 22:43:22|   Array #1 of 7...done
> 20100928 22:43:22|   Array #2 of 7...
> 20100928 22:43:23|   Array #2 of 7...done
> 20100928 22:43:23|   Array #3 of 7...
> 20100928 22:43:24|   Array #3 of 7...done
> 20100928 22:43:24|   Array #4 of 7...
> 20100928 22:43:26|   Array #4 of 7...done
> 20100928 22:43:26|   Array #5 of 7...
> 20100928 22:43:27|   Array #5 of 7...done
> 20100928 22:43:27|   Array #6 of 7...
> 20100928 22:43:28|   Array #6 of 7...done
> 20100928 22:43:28|   Array #7 of 7...
> 20100928 22:43:30|   Array #7 of 7...done
>               used (Mb) gc trigger  (Mb)  max used  (Mb)
>    Ncells  1158299 61.9    4930533 263.4  17756025 948.3
>    Vcells 11274772 86.1   35523968 271.1 106800686 814.9
> 20100928 22:43:31|  Extracting 25000 random PM intensities across CEL
> set...done
> 20100928 22:43:31|  Extracting probe affinities and fitting linear model...
>               used (Mb) gc trigger  (Mb)  max used  (Mb)
>    Ncells  1158298 61.9    3944426 210.7  17756025 948.3
>    Vcells 11287264 86.2   35523968 271.1 106800686 814.9
> 20100928 22:43:32|   Fitting the GCRMA background linear model...
>      num [1:25000] 5.39 8.46 8.41 6.89 8.05 ...
>      num [1:25000] 0.485 -0.764 1.766 -0.857 0.344 ...
>
>     Call:
>     lm(formula = pm.random2 ~ aff)
>
>     Coefficients:
>     (Intercept)          aff
>          6.5646       0.4193
>
> 20100928 22:43:32|   Fitting the GCRMA background linear model...done
> 20100928 22:43:32|  Extracting probe affinities and fitting linear
> model...done
> 20100928 22:43:32| Estimating specific binding parameters...done
> 20100928 22:43:32| Adjusting 7 arrays...
> 20100928 22:43:32|  Array #1 of 7...
>    AffymetrixCelFile:
>    Name: DK Litter D15 P1_(MoEx-1_0-st-v1)
>    Tags:
>    Full name: DK Litter D15 P1_(MoEx-1_0-st-v1)
>    Pathname: probeData/Exon Data,OBC/MoEx-1_0-st-v1/DK Litter D15
> P1_(MoEx-1_0-st-v1).CEL
>    File size: 62.50 MB (65536703 bytes)
>    RAM: 0.00 MB
>    File format: v4 (binary; XDA)
>    Platform: Affymetrix
>    Chip type: MoEx-1_0-st-v1
>    Timestamp: 2010-09-28 14:26:37
> 20100928 22:43:32|   Obtaining PM and MM signals and affinities...
> 20100928 22:45:16|   Obtaining PM and MM signals and affinities...done
> 20100928 22:45:16|   Estimating non-specific binding parameters...
> Error in quantile.default(a1, 0.001) :
>   missing values and NaN's not allowed if 'na.rm' is FALSE
> 20100928 22:45:16|  Array #1 of 7...done
> 20100928 22:45:16| Adjusting 7 arrays...done
> 20100928 22:45:16|Background correcting data set...done
>> traceback()
> 15: stop("missing values and NaN's not allowed if 'na.rm' is FALSE")
> 14: quantile.default(a1, 0.001)
> 13: quantile(a1, 0.001)
> 12: seq(quantile(a1, 0.001), quantile(a1, 0.999), len = 26)
> 11: cut.default(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1,
>         0.999), len = 26), Inf))
> 10: cut(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1, 0.999),
>         len = 26), Inf))
> 9: bg.parameters.ns(ncs[index.affinities], anc, apm)
> 8: gcrma::bg.adjust.affinities(pm, mm, apm, amm, index.affinities =
> 1:length(pm),
>        k = k, fast = fast)
> 7: bgAdjustGcrma.AffymetrixCelFile(df, path = path, type = type,
>        indicesNegativeControl = indicesNegativeControl, affinities =
> affinities,
>        gsbAdjust = gsbAdjust, parametersGsb = parametersGsb, k = k,
>        rho = rho, stretch = stretch, fast = fast, overwrite = overwrite,
>        skip = skip, ..., verbose = less(verbose), .deprecated = .deprecated)
> 6: bgAdjustGcrma(df, path = path, type = type, indicesNegativeControl =
> indicesNegativeControl,
>        affinities = affinities, gsbAdjust = gsbAdjust, parametersGsb =
> parametersGsb,
>        k = k, rho = rho, stretch = stretch, fast = fast, overwrite =
> overwrite,
>        skip = skip, ..., verbose = less(verbose), .deprecated = .deprecated)
> 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 3: do.call("bgAdjustGcrma", args = args)
> 2: process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose =
> verbose,
>        na.rm = "TRUE")
> 1: process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
>
> Is it somehow  possible to replace the NaN and missing values to some other
> value (like the mean or median or some small number close to 0)?

It is good that we made progress.  The new error looks like a "bug" in
the sense that that piece of code does not expect NAs to appear.  I
have to looking into this and figure out if NAs can indeed be expected
of if they are incorrectly introduced earlier in the pipeline or not.
 I will also go back to our redundancy tests and check, because we do
not detect this problem there.  If NAs should be allowed, the fix
should be simple, but has to be done by me updating the code.

I'll get back to your when I've done this.

> Also I am getting some output in the probeData folder as:
> probeData/Exon Data,OBC/MoEx-1_0-st-v1/(all the *.cel files) and
> probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa.
> What are this outputs corresponds to?

That file contains the GCRMA probe affinities computed from the CDF
and the probe-sequence file.  Consider it as an internal file that is
saved to disk so that the next time you run the pipeline, if redone,
it be found and the processing will be much faster.

Sorry about all these issues.  As I almost write in every
correspondence related to gcRMA processing - the inner code was
written in the early days and specifically for a few chip types.
After that new chip types came around and things became a bit shaky.
However and although not really visible to the end user, we are slowly
updating the code and moving to a more robust and generic solution.
What the end user probably sees is more and more informative error
messages.  So, base with us.

Cheers,

Henrik

> Again thank you for the help.
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> On Tue, Sep 28, 2010 at 1:47 AM, Henrik Bengtsson <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> sorry, my mistake.  I missed that you already did this.
>>
>> You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
>> You can download it from Affymetrix and you'll find a link to their
>> support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
>> .  Download it (something like "MoEx-1_0-st-v1 Probe Sequences,
>> tabular format (130 MB, 3/19/08)") and place it in
>> annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is
>> correct by trying the following:
>>
>> > library("aroma.affymetrix");
>> > ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
>> > ptf
>> AffymetrixProbeTabFile:
>> Name: MoEx-1_0-st-v1
>> Tags:
>> Full name: MoEx-1_0-st-v1
>> Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab
>> File size: 460.47 MB (482839635 bytes)
>> RAM: 0.01 MB
>> Number of data rows: NA
>> Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
>> 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
>> 'targetStrandedness', 'category'
>> Number of text lines: NA
>> AffymetrixCdfFile:
>> Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> Filename: MoEx-1_0-st-v1.cdf
>> Filesize: 274.30MB
>> Chip type: MoEx-1_0-st-v1
>> RAM: 0.00MB
>> File format: v4 (binary; XDA)
>> Dimension: 2560x2560
>> Number of cells: 6553600
>> Number of units: 1257006
>> Cells per unit: 5.21
>> Number of QC units: 0
>>
>> If you get that to work, then your script should work.
>>
>> Let me now if this solved your problem.
>>
>> /Henrik
>>
>> On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee
>> <[hidden email]> wrote:
>> > Respected Dr Bengtsson,
>> > My codes and outputs are as follows:
>> >> source("http://aroma-project.org/hbLite.R");
>> >> hbInstall("aroma.affymetrix")
>> >> source("http://aroma-project.org/hbLite.R");
>> >> hbInstall("aroma.cn")
>> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> dataSet <- "Exon Data"
>> >> chipType <- "MoEx-1_0-st-v1"
>> >> cdf <-
>> >> AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> >> print(cdf)
>> > AffymetrixCdfFile:
>> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> > Filesize: 30.53MB
>> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> > RAM: 0.00MB
>> > File format: v4 (binary; XDA)
>> > Dimension: 2560x2560
>> > Number of cells: 6553600
>> > Number of units: 17831
>> > Cells per unit: 367.54
>> > Number of QC units: 1
>> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >> print(csR)
>> > AffymetrixCelSet:
>> > Name: Exon Data
>> > Tags:
>> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> > Platform: Affymetrix
>> > Chip type: MoEx-1_0-st-v1
>> > Number of arrays: 7
>> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> > Total file size: 440.55MB
>> > RAM: 0.01MB
>> >> cdf <- getCdf(csR)
>> >> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>> >> setCdf(csR, cdfS)
>> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >> print(bc)
>> > GcRmaBackgroundCorrection:
>> > Data set: Exon Data
>> > Input tags:
>> > User tags: *
>> > Asterisk ('*') tags: GRBC
>> > Output tags: GRBC
>> > Number of files: 7 (440.55MB)
>> > Platform: Affymetrix
>> > Chip type: MoEx-1_0-st-v1
>> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
>> > indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
>> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> > Is done: FALSE
>> > RAM: 0.00MB
>> >> csB <- process(bc, verbose=verbose)
>> > 20100927 16:31:40|Background correcting data set...
>> > 20100927 16:31:40| Computing probe affinities...
>> > 20100927 16:31:40|  Computing GCRMA probe affinities for 1257006
>> > units...
>> > 20100927 16:31:40|   Identify PMs and MMs among the CDF cell indices...
>> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >        Mode   FALSE    TRUE    NA's
>> >     logical  334476 4931683       0
>> > 20100927 16:33:30|    MMs are defined as non-PMs
>> > 20100927 16:33:30|    Number of PMs: 4931683
>> > 20100927 16:33:30|    Number of MMs: 334476
>> > 20100927 16:33:30|   Identify PMs and MMs among the CDF cell
>> > indices...done
>> > 20100927 16:33:30|   Reading probe-sequence data...
>> > 20100927 16:33:30|    Retrieving probe-sequence data...
>> > 20100927 16:33:30|     Chip type (full): MoEx-1_0-st-v1
>> > 20100927 16:33:30|     Locating probe-tab file...
>> > 20100927 16:33:30|      Chip type: MoEx-1_0-st-v1
>> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> > <environment>,
>> >  :
>> >
>> > [2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
>> > deprectated (v1) search rules:
>> >   at throw(Exception(...))
>> >   at throw.default("Found probe-tab file only by means of deprectated
>> > (v1
>> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> > search
>> >   at method(static, ...)
>> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>> >   at method(static, ...)
>> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> > les
>> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> > ver
>> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> > less(verbos
>> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> > Data,GRBC/
>> >   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>> >   at do.call("bgAdjustGcrma", args = args)
>> >   at process.GcRmaBackgroundCorrection(
>> > 20100927 16:33:30|     Locating probe-tab file...done
>> > 20100927 16:33:30|    Retrieving probe-sequence data...done
>> > 20100927 16:33:30|   Reading probe-sequence data...done
>> > 20100927 16:33:30|  Computing GCRMA probe affinities for 1257006
>> > units...done
>> > 20100927 16:33:30| Computing probe affinities...done
>> > 20100927 16:33:30|Background correcting data set...done
>> >> traceback()
>> > 17: throw.Exception(Exception(...))
>> > 16: throw(Exception(...))
>> > 15: throw.default("Found probe-tab file only by means of deprectated
>> > (v1)
>> > search rules: ",
>> >         pathname)
>> > 14: throw("Found probe-tab file only by means of deprectated (v1) search
>> > rules: ",
>> >         pathname)
>> > 13: method(static, ...)
>> > 12: AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>> >         ...)
>> > 11: method(static, ...)
>> > 10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> > less(verbose,
>> >         100))
>> > 9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>> > verbose)
>> > 8: getProbeSequenceData(this, safe = safe, verbose = verbose)
>> > 7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> >        verbose = less(verbose))
>> > 6: computeAffinities(cdf, paths = probePath, ..., verbose =
>> > less(verbose))
>> > 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> > Data,GRBC/MoEx-1_0-st-v1",
>> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
>> > NULL,
>> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >        gsbParameters = NULL, .deprecated = FALSE)
>> > 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
>> > NULL,
>> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >        gsbParameters = NULL, .deprecated = FALSE)
>> > 3: do.call("bgAdjustGcrma", args = args)
>> > 2: process.GcRmaBackgroundCorrection(bc, verbose = verbose)
>> > 1: process(bc, verbose = verbose)
>> >> sessionInfo()
>> > R version 2.11.1 (2010-05-31)
>> > x86_64-apple-darwin9.8.0
>> > locale:
>> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> > attached base packages:
>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>> > other attached packages:
>> >  [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7        affxparser_1.20.0
>> >  [4] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>> >  [7] matrixStats_0.2.1      R.rsp_0.4.0            R.filesets_0.9.0
>> > [10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.2
>> > [13] R.oo_1.7.4             R.methodsS3_1.2.1
>> > loaded via a namespace (and not attached):
>> > [1] tools_2.11.1
>> > The working directory is desktop and the path for the cdf file and the
>> > raw
>> > data is as follows:
>> >
>> > /Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> > ( I have several other cdf files
>> >
>> > like MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
>> > and MoEx-1_0-st-v1.cdf in the same directory.)
>> > /Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/
>> > DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P2_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P3_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P6_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P14_(MoEx-1_0-st-v1).CEL
>> > Moreover I am following the thread and implementing the code you
>> > suggested
>> > there but it is not working with my dataset. Please help.
>> > Thank you,
>> > Prithish Banerjee,
>> > Graduate Research Assistant,
>> > Department of Statistics,
>> > West Virginia University.
>> >
>> > On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson <[hidden email]>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> first of all, for this chip type you need to specify:
>> >>
>> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> >>
>> >> Moreover, you cannot use the custom CDF in the
>> >> GcRmaBackgroundCorrection step, and have to do the follow workaround
>> >> illustrated in the below example:
>> >>
>> >>
>> >> library("aroma.affymetrix");
>> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> dataSet <- "Affymetrix-Tissues";
>> >> chipType <- "MoEx-1_0-st-v1";
>> >>
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> # Setup data set
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> cdf <- AffymetrixCdfFile$byChipType(chipType,
>> >> tags="coreR1,A20080718,MR");
>> >> print(cdf);
>> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
>> >> print(csR);
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> # gcRMA-style background correction
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> # Currently, you must use the standard CDF file.
>> >> cdf <- getCdf(csR);
>> >> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
>> >> setCdf(csR, cdfS);
>> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> >> print(bc);
>> >> csB <- process(bc, verbose=verbose);
>> >> print(csB);
>> >> # Now, use the custom CDF in what follows
>> >> setCdf(csB, cdf);
>> >> print(csB);
>> >>
>> >> Yes, those last steps are rather confusing - we're working on updating
>> >> the code so you don't have to do that yourself.
>> >>
>> >> FYI, the above solution/workaround was resolved in thread 'GCRMA
>> >> normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
>> >> http://goo.gl/cniq.
>> >>
>> >> Hope this helps
>> >>
>> >> /Henrik
>> >>
>> >> On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
>> >> <[hidden email]> wrote:
>> >> > Hi All,
>> >> > I am trying to normalize a mouse exon array dataset using GCRMA
>> >> > normalization technique. I have exactly followed all the necessary
>> >> > steps
>> >> > for
>> >> > storing the dataset and the cdf file. the code and the output I am
>> >> > using
>> >> > are
>> >> > as follows:
>> >> >
>> >> > source("http://aroma-project.org/hbLite.R");
>> >> >
>> >> > hbInstall("aroma.affymetrix")
>> >> >
>> >> > source("http://aroma-project.org/hbLite.R");
>> >> >
>> >> > hbInstall("aroma.cn")
>> >> >
>> >> > verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> >
>> >> > dataSet <- "Exon Data" [the path in the working directory is
>> >> > rawData/Exon
>> >> > Data/MoEx-1_0-st-v1/*.CEL files]
>> >> >
>> >> > chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
>> >> >
>> >> >
>> >> > annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>> >> >
>> >> > cdf <-
>> >> > AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> >> > [converted to binary using convertCdf command]
>> >> >
>> >> > print(cdf)
>> >> >
>> >> > AffymetrixCdfFile:
>> >> >
>> >> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> >> >
>> >> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> >> >
>> >> > Filesize: 30.53MB
>> >> >
>> >> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> >> >
>> >> > RAM: 0.00MB
>> >> >
>> >> > File format: v4 (binary; XDA)
>> >> >
>> >> > Dimension: 2560x2560
>> >> >
>> >> > Number of cells: 6553600
>> >> >
>> >> > Number of units: 17831
>> >> >
>> >> > Cells per unit: 367.54
>> >> >
>> >> > Number of QC units: 1
>> >> >
>> >> > csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >> >
>> >> > print(csR)
>> >> >
>> >> > AffymetrixCelSet:
>> >> >
>> >> > Name: Exon Data
>> >> >
>> >> > Tags:
>> >> >
>> >> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> >> >
>> >> > Platform: Affymetrix
>> >> >
>> >> > Chip type: MoEx-1_0-st-v1
>> >> >
>> >> > Number of arrays: 7
>> >> >
>> >> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> >> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> >> >
>> >> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> >> >
>> >> > Total file size: 440.55MB
>> >> >
>> >> > RAM: 0.01MB
>> >> >
>> >> > cdf <- getCdf(csR)
>> >> >
>> >> > cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf,
>> >> > fullname=FALSE))
>> >> >
>> >> > setCdf(csR, cdfS)
>> >> >
>> >> > bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >> >
>> >> > print(bc)
>> >> >
>> >> > GcRmaBackgroundCorrection:
>> >> >
>> >> > Data set: Exon Data
>> >> >
>> >> > Input tags:
>> >> >
>> >> > User tags: *
>> >> >
>> >> > Asterisk ('*') tags: GRBC
>> >> >
>> >> > Output tags: GRBC
>> >> >
>> >> > Number of files: 7 (440.55MB)
>> >> >
>> >> > Platform: Affymetrix
>> >> >
>> >> > Chip type: MoEx-1_0-st-v1
>> >> >
>> >> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
>> >> > indicesNegativeControl: NULL, affinities: NULL, type: chr
>> >> > "affinities",
>> >> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>> >> >
>> >> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> >> >
>> >> > Is done: FALSE
>> >> >
>> >> > RAM: 0.00MB
>> >> >
>> >> > csB <- process(bc, verbose=verbose)
>> >> >
>> >> > 20100923 13:24:12|Background correcting data set...
>> >> >
>> >> > 20100923 13:24:12| Computing probe affinities...
>> >> >
>> >> > 20100923 13:24:12|  Computing GCRMA probe affinities for 1257006
>> >> > units...
>> >> >
>> >> > 20100923 13:24:12|   Identify PMs and MMs among the CDF cell
>> >> > indices...
>> >> >
>> >> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >> >
>> >> >        Mode   FALSE    TRUE    NA's
>> >> >
>> >> >     logical  334476 4931683       0
>> >> >
>> >> > 20100923 13:25:57|    MMs are defined as non-PMs
>> >> >
>> >> > 20100923 13:25:57|    Number of PMs: 4931683
>> >> >
>> >> > 20100923 13:25:57|    Number of MMs: 334476
>> >> >
>> >> > 20100923 13:25:57|   Identify PMs and MMs among the CDF cell
>> >> > indices...done
>> >> >
>> >> > 20100923 13:25:57|   Reading probe-sequence data...
>> >> >
>> >> > 20100923 13:25:57|    Retrieving probe-sequence data...
>> >> >
>> >> > 20100923 13:25:57|     Chip type (full): MoEx-1_0-st-v1
>> >> >
>> >> > 20100923 13:25:57|     Locating probe-tab file...
>> >> >
>> >> > 20100923 13:25:57|      Chip type: MoEx-1_0-st-v1
>> >> >
>> >> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> >> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> >> > <environment>,
>> >> >  :
>> >> >
>> >> >
>> >> >
>> >> > [2010-09-23 13:25:57] Exception: Found probe-tab file only by means
>> >> > of
>> >> > deprectated (v1) search rules:
>> >> >
>> >> >   at throw(Exception(...))
>> >> >
>> >> >   at throw.default("Found probe-tab file only by means of deprectated
>> >> > (v1
>> >> >
>> >> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> >> > search
>> >> >
>> >> >   at method(static, ...)
>> >> >
>> >> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>> >> > ...)
>> >> >
>> >> >   at method(static, ...)
>> >> >
>> >> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> >> > les
>> >> >
>> >> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe,
>> >> > verbose =
>> >> >
>> >> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >> >
>> >> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> >> > ver
>> >> >
>> >> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> >> > less(verbos
>> >> >
>> >> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> >> > Data,GRBC/
>> >> >
>> >> >   at bgAdjustGcrma(NA, path = "probeData/Exon
>> >> > Data,GRBC/MoEx-1_0-st-v1",
>> >> >
>> >> >   at do.call("bgAdjustGcrma", args = args)
>> >> >
>> >> >   at process.GcRmaBackgroundCorrection(
>> >> >
>> >> > 20100923 13:25:57|     Locating probe-tab file...done
>> >> >
>> >> > 20100923 13:25:57|    Retrieving probe-sequence data...done
>> >> >
>> >> > 20100923 13:25:57|   Reading probe-sequence data...done
>> >> >
>> >> > 20100923 13:25:57|  Computing GCRMA probe affinities for 1257006
>> >> > units...done
>> >> >
>> >> > 20100923 13:25:57| Computing probe affinities...done
>> >> >
>> >> > 20100923 13:25:57|Background correcting data set...done
>> >> >
>> >> > Could anyone please enlighten me with the type of the error? I will
>> >> > be
>> >> > highly obliged if anyone please help me with this problem.
>> >> >
>> >> > Thank you.
>> >> >
>> >> > Prithish Banerjee.
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> > latest
>> >> > version of the package, 2) to report the output of sessionInfo() and
>> >> > traceback(), and 3) to post a complete code example.
>> >> >
>> >> >
>> >> > You received this message because you are subscribed to the Google
>> >> > Groups
>> >> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> >> > To post to this group, send email to
>> >> > [hidden email]
>> >> > To unsubscribe and other options, go to
>> >> > http://www.aroma-project.org/forum/
>> >> >
>> >>
>> >> --
>> >> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> latest version of the package, 2) to report the output of sessionInfo()
>> >> and
>> >> traceback(), and 3) to post a complete code example.
>> >>
>> >>
>> >> You received this message because you are subscribed to the Google
>> >> Groups
>> >> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> >> To post to this group, send email to [hidden email]
>> >> To unsubscribe and other options, go to
>> >> http://www.aroma-project.org/forum/
>> >
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to [hidden email]
>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Prithish Banerjee
Respected Dr Bengtsson,

Thank you for your help. I was working with the human-exon dataset and found that all the probe sequence tabular files are in ASCII format( from affymetrix). Is it possible to convert the ptf files to binary same as the cdf files??

Thank you,
Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.

On Wed, Sep 29, 2010 at 3:14 PM, Henrik Bengtsson <[hidden email]> wrote:
Hi.

On Wed, Sep 29, 2010 at 10:32 AM, Prithish Banerjee
<[hidden email]> wrote:
> Respected Dr Bengtsson,
> Thank you for the help. I have done what you have suggested and the
> following output is as follows:
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.affymetrix")
>
> source("http://aroma-project.org/hbLite.R");
>
> hbInstall("aroma.cn")
>
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>
> dataSet <- "Exon Data"
>
> chipType <- "MoEx-1_0-st-v1"
>
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>
> print(cdf)
>
> ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
>
> print(ptf)
>
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>
> print(csR)
>
> cdf <- getCdf(csR)
>
> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>
> setCdf(csR, cdfS)
>
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>
> print(bc)
>
> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
> 20100928 22:40:59|Background correcting data set...
> 20100928 22:41:09| Computing probe affinities...
> 20100928 22:41:09|  Reading saved affinities: probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...
> 20100928 22:41:10|  Reading saved affinities: probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...done
> 20100928 22:41:10|  RAM: 50.00MB
> 20100928 22:41:10| Computing probe affinities...done
> 20100928 22:41:10| Background correcting data set...
> 20100928 22:41:16|  Already background corrected for "optical" effects
> 20100928 22:41:16| Background correcting data set...done
> 20100928 22:41:16| Estimating specific binding parameters...
> 20100928 22:41:16|  Extracting PM indices...
> 20100928 22:41:16|   Reading cell indices from CDF file...
> 20100928 22:41:16|    Pathname:
> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf
> 20100928 22:41:16|    Units:
>      NULL
> 20100928 22:41:16|    lapplyInChunks()...
> 20100928 22:41:16|     Number of elements per chunk: 1e+05
> 20100928 22:41:16|     Chunk #1 of 13...
> 20100928 22:41:16|      Elements:
>        int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
> 20100928 22:41:16|      Querying CDF file...
> 20100928 22:41:20|      Querying CDF file...done
> 20100928 22:41:21|      Restructuring...
> 20100928 22:41:21|      Restructuring...done
>                  used (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058626  110    6907341 368.9  17756025 948.3
>       Vcells 14800385  113   55506200 423.5 106800686 814.9
> 20100928 22:41:21|     Chunk #1 of 13...done
> 20100928 22:41:21|     Chunk #2 of 13...
> 20100928 22:41:21|      Elements:
>        int [1:100000] 100001 100002 100003 100004 100005 100006 100007
> 100008 100009 100010 ...
> 20100928 22:41:21|      Querying CDF file...
> 20100928 22:41:25|      Querying CDF file...done
> 20100928 22:41:26|      Restructuring...
> 20100928 22:41:26|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058632 110.0    6907341 368.9  17756025 948.3
>       Vcells 14946933 114.1   44404960 338.8 106800686 814.9
> 20100928 22:41:26|     Chunk #2 of 13...done
> 20100928 22:41:26|     Chunk #3 of 13...
> 20100928 22:41:26|      Elements:
>        int [1:100000] 200001 200002 200003 200004 200005 200006 200007
> 200008 200009 200010 ...
> 20100928 22:41:26|      Querying CDF file...
> 20100928 22:41:30|      Querying CDF file...done
> 20100928 22:41:30|      Restructuring...
> 20100928 22:41:30|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058634 110.0    6907341 368.9  17756025 948.3
>       Vcells 15101344 115.3   44404960 338.8 106800686 814.9
> 20100928 22:41:31|     Chunk #3 of 13...done
> 20100928 22:41:31|     Chunk #4 of 13...
> 20100928 22:41:31|      Elements:
>        int [1:100000] 300001 300002 300003 300004 300005 300006 300007
> 300008 300009 300010 ...
> 20100928 22:41:31|      Querying CDF file...
> 20100928 22:41:35|      Querying CDF file...done
> 20100928 22:41:35|      Restructuring...
> 20100928 22:41:35|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058634 110.0    6907341 368.9  17756025 948.3
>       Vcells 15249056 116.4   44404960 338.8 106800686 814.9
> 20100928 22:41:36|     Chunk #4 of 13...done
> 20100928 22:41:36|     Chunk #5 of 13...
> 20100928 22:41:36|      Elements:
>        int [1:100000] 400001 400002 400003 400004 400005 400006 400007
> 400008 400009 400010 ...
> 20100928 22:41:36|      Querying CDF file...
> 20100928 22:41:40|      Querying CDF file...done
> 20100928 22:41:40|      Restructuring...
> 20100928 22:41:40|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058635 110.0    6907341 368.9  17756025 948.3
>       Vcells 15397125 117.5   44404960 338.8 106800686 814.9
> 20100928 22:41:40|     Chunk #5 of 13...done
> 20100928 22:41:40|     Chunk #6 of 13...
> 20100928 22:41:40|      Elements:
>        int [1:100000] 500001 500002 500003 500004 500005 500006 500007
> 500008 500009 500010 ...
> 20100928 22:41:40|      Querying CDF file...
> 20100928 22:41:44|      Querying CDF file...done
> 20100928 22:41:45|      Restructuring...
> 20100928 22:41:45|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058637 110.0    6907341 368.9  17756025 948.3
>       Vcells 15541779 118.6   44404960 338.8 106800686 814.9
> 20100928 22:41:45|     Chunk #6 of 13...done
> 20100928 22:41:45|     Chunk #7 of 13...
> 20100928 22:41:45|      Elements:
>        int [1:100000] 600001 600002 600003 600004 600005 600006 600007
> 600008 600009 600010 ...
> 20100928 22:41:45|      Querying CDF file...
> 20100928 22:41:49|      Querying CDF file...done
> 20100928 22:41:50|      Restructuring...
> 20100928 22:41:50|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058637 110.0    6907341 368.9  17756025 948.3
>       Vcells 15690489 119.8   44404960 338.8 106800686 814.9
> 20100928 22:41:50|     Chunk #7 of 13...done
> 20100928 22:41:50|     Chunk #8 of 13...
> 20100928 22:41:50|      Elements:
>        int [1:100000] 700001 700002 700003 700004 700005 700006 700007
> 700008 700009 700010 ...
> 20100928 22:41:50|      Querying CDF file...
> 20100928 22:41:54|      Querying CDF file...done
> 20100928 22:41:54|      Restructuring...
> 20100928 22:41:54|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058638 110.0    6907341 368.9  17756025 948.3
>       Vcells 15837280 120.9   44404960 338.8 106800686 814.9
> 20100928 22:41:55|     Chunk #8 of 13...done
> 20100928 22:41:55|     Chunk #9 of 13...
> 20100928 22:41:55|      Elements:
>        int [1:100000] 800001 800002 800003 800004 800005 800006 800007
> 800008 800009 800010 ...
> 20100928 22:41:55|      Querying CDF file...
> 20100928 22:41:59|      Querying CDF file...done
> 20100928 22:41:59|      Restructuring...
> 20100928 22:41:59|      Restructuring...done
>                  used (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058640  110    6907341 368.9  17756025 948.3
>       Vcells 15987604  122   44404960 338.8 106800686 814.9
> 20100928 22:41:59|     Chunk #9 of 13...done
> 20100928 22:41:59|     Chunk #10 of 13...
> 20100928 22:41:59|      Elements:
>        int [1:100000] 900001 900002 900003 900004 900005 900006 900007
> 900008 900009 900010 ...
> 20100928 22:41:59|      Querying CDF file...
> 20100928 22:42:04|      Querying CDF file...done
> 20100928 22:42:04|      Restructuring...
> 20100928 22:42:04|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2066219 110.4    6907341 368.9  17756025 948.3
>       Vcells 16292565 124.4   44404960 338.8 106800686 814.9
> 20100928 22:42:04|     Chunk #10 of 13...done
> 20100928 22:42:04|     Chunk #11 of 13...
> 20100928 22:42:04|      Elements:
>        int [1:100000] 1000001 1000002 1000003 1000004 1000005 1000006
> 1000007 1000008 1000009 1000010 ...
> 20100928 22:42:05|      Querying CDF file...
> 20100928 22:42:08|      Querying CDF file...done
> 20100928 22:42:09|      Restructuring...
> 20100928 22:42:09|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058641 110.0    6907341 368.9  17756025 948.3
>       Vcells 16431821 125.4   44404960 338.8 106800686 814.9
> 20100928 22:42:09|     Chunk #11 of 13...done
> 20100928 22:42:09|     Chunk #12 of 13...
> 20100928 22:42:09|      Elements:
>        int [1:100000] 1100001 1100002 1100003 1100004 1100005 1100006
> 1100007 1100008 1100009 1100010 ...
> 20100928 22:42:09|      Querying CDF file...
> 20100928 22:42:13|      Querying CDF file...done
> 20100928 22:42:14|      Restructuring...
> 20100928 22:42:14|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  2058642 110.0    6907341 368.9  17756025 948.3
>       Vcells 16577525 126.5   44404960 338.8 106800686 814.9
> 20100928 22:42:14|     Chunk #12 of 13...done
> 20100928 22:42:14|     Chunk #13 of 13...
> 20100928 22:42:14|      Elements:
>        int [1:57006] 1200001 1200002 1200003 1200004 1200005 1200006 1200007
> 1200008 1200009 1200010 ...
> 20100928 22:42:14|      Querying CDF file...
> 20100928 22:42:16|      Querying CDF file...done
> 20100928 22:42:17|      Restructuring...
> 20100928 22:42:17|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>       Ncells  1671697  89.3    5525872 295.2  17756025 948.3
>       Vcells 16271204 124.2   44404960 338.8 106800686 814.9
> 20100928 22:42:17|     Chunk #13 of 13...done
> 20100928 22:42:17|    lapplyInChunks()...done
> 20100928 22:42:17|   Reading cell indices from CDF file...done
>               used  (Mb) gc trigger  (Mb)  max used  (Mb)
>    Ncells  1158492  61.9    4420697 236.1  17756025 948.3
>    Vcells 13870500 105.9   44404960 338.8 106800686 814.9
> 20100928 22:42:17|   readUnits.AffymetrixCdfFile(): Updating cache
> 20100928 22:43:21|  Extracting PM indices...done
>              used (Mb) gc trigger  (Mb)  max used  (Mb)
>   Ncells  1158442 61.9    6163167 329.2  17756025 948.3
>   Vcells 11250131 85.9   35523968 271.1 106800686 814.9
> 20100928 22:43:22|  Extracting 25000 random PM intensities across CEL set...
> 20100928 22:43:22|   Array #1 of 7...
> 20100928 22:43:22|   Array #1 of 7...done
> 20100928 22:43:22|   Array #2 of 7...
> 20100928 22:43:23|   Array #2 of 7...done
> 20100928 22:43:23|   Array #3 of 7...
> 20100928 22:43:24|   Array #3 of 7...done
> 20100928 22:43:24|   Array #4 of 7...
> 20100928 22:43:26|   Array #4 of 7...done
> 20100928 22:43:26|   Array #5 of 7...
> 20100928 22:43:27|   Array #5 of 7...done
> 20100928 22:43:27|   Array #6 of 7...
> 20100928 22:43:28|   Array #6 of 7...done
> 20100928 22:43:28|   Array #7 of 7...
> 20100928 22:43:30|   Array #7 of 7...done
>               used (Mb) gc trigger  (Mb)  max used  (Mb)
>    Ncells  1158299 61.9    4930533 263.4  17756025 948.3
>    Vcells 11274772 86.1   35523968 271.1 106800686 814.9
> 20100928 22:43:31|  Extracting 25000 random PM intensities across CEL
> set...done
> 20100928 22:43:31|  Extracting probe affinities and fitting linear model...
>               used (Mb) gc trigger  (Mb)  max used  (Mb)
>    Ncells  1158298 61.9    3944426 210.7  17756025 948.3
>    Vcells 11287264 86.2   35523968 271.1 106800686 814.9
> 20100928 22:43:32|   Fitting the GCRMA background linear model...
>      num [1:25000] 5.39 8.46 8.41 6.89 8.05 ...
>      num [1:25000] 0.485 -0.764 1.766 -0.857 0.344 ...
>
>     Call:
>     lm(formula = pm.random2 ~ aff)
>
>     Coefficients:
>     (Intercept)          aff
>          6.5646       0.4193
>
> 20100928 22:43:32|   Fitting the GCRMA background linear model...done
> 20100928 22:43:32|  Extracting probe affinities and fitting linear
> model...done
> 20100928 22:43:32| Estimating specific binding parameters...done
> 20100928 22:43:32| Adjusting 7 arrays...
> 20100928 22:43:32|  Array #1 of 7...
>    AffymetrixCelFile:
>    Name: DK Litter D15 P1_(MoEx-1_0-st-v1)
>    Tags:
>    Full name: DK Litter D15 P1_(MoEx-1_0-st-v1)
>    Pathname: probeData/Exon Data,OBC/MoEx-1_0-st-v1/DK Litter D15
> P1_(MoEx-1_0-st-v1).CEL
>    File size: 62.50 MB (65536703 bytes)
>    RAM: 0.00 MB
>    File format: v4 (binary; XDA)
>    Platform: Affymetrix
>    Chip type: MoEx-1_0-st-v1
>    Timestamp: 2010-09-28 14:26:37
> 20100928 22:43:32|   Obtaining PM and MM signals and affinities...
> 20100928 22:45:16|   Obtaining PM and MM signals and affinities...done
> 20100928 22:45:16|   Estimating non-specific binding parameters...
> Error in quantile.default(a1, 0.001) :
>   missing values and NaN's not allowed if 'na.rm' is FALSE
> 20100928 22:45:16|  Array #1 of 7...done
> 20100928 22:45:16| Adjusting 7 arrays...done
> 20100928 22:45:16|Background correcting data set...done
>> traceback()
> 15: stop("missing values and NaN's not allowed if 'na.rm' is FALSE")
> 14: quantile.default(a1, 0.001)
> 13: quantile(a1, 0.001)
> 12: seq(quantile(a1, 0.001), quantile(a1, 0.999), len = 26)
> 11: cut.default(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1,
>         0.999), len = 26), Inf))
> 10: cut(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1, 0.999),
>         len = 26), Inf))
> 9: bg.parameters.ns(ncs[index.affinities], anc, apm)
> 8: gcrma::bg.adjust.affinities(pm, mm, apm, amm, index.affinities =
> 1:length(pm),
>        k = k, fast = fast)
> 7: bgAdjustGcrma.AffymetrixCelFile(df, path = path, type = type,
>        indicesNegativeControl = indicesNegativeControl, affinities =
> affinities,
>        gsbAdjust = gsbAdjust, parametersGsb = parametersGsb, k = k,
>        rho = rho, stretch = stretch, fast = fast, overwrite = overwrite,
>        skip = skip, ..., verbose = less(verbose), .deprecated = .deprecated)
> 6: bgAdjustGcrma(df, path = path, type = type, indicesNegativeControl =
> indicesNegativeControl,
>        affinities = affinities, gsbAdjust = gsbAdjust, parametersGsb =
> parametersGsb,
>        k = k, rho = rho, stretch = stretch, fast = fast, overwrite =
> overwrite,
>        skip = skip, ..., verbose = less(verbose), .deprecated = .deprecated)
> 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
> Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
> NULL,
>        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>        gsbParameters = NULL, .deprecated = FALSE)
> 3: do.call("bgAdjustGcrma", args = args)
> 2: process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose =
> verbose,
>        na.rm = "TRUE")
> 1: process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
>
> Is it somehow  possible to replace the NaN and missing values to some other
> value (like the mean or median or some small number close to 0)?

It is good that we made progress.  The new error looks like a "bug" in
the sense that that piece of code does not expect NAs to appear.  I
have to looking into this and figure out if NAs can indeed be expected
of if they are incorrectly introduced earlier in the pipeline or not.
 I will also go back to our redundancy tests and check, because we do
not detect this problem there.  If NAs should be allowed, the fix
should be simple, but has to be done by me updating the code.

I'll get back to your when I've done this.

> Also I am getting some output in the probeData folder as:
> probeData/Exon Data,OBC/MoEx-1_0-st-v1/(all the *.cel files) and
> probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa.
> What are this outputs corresponds to?

That file contains the GCRMA probe affinities computed from the CDF
and the probe-sequence file.  Consider it as an internal file that is
saved to disk so that the next time you run the pipeline, if redone,
it be found and the processing will be much faster.

Sorry about all these issues.  As I almost write in every
correspondence related to gcRMA processing - the inner code was
written in the early days and specifically for a few chip types.
After that new chip types came around and things became a bit shaky.
However and although not really visible to the end user, we are slowly
updating the code and moving to a more robust and generic solution.
What the end user probably sees is more and more informative error
messages.  So, base with us.

Cheers,

Henrik

> Again thank you for the help.
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> On Tue, Sep 28, 2010 at 1:47 AM, Henrik Bengtsson <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> sorry, my mistake.  I missed that you already did this.
>>
>> You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
>> You can download it from Affymetrix and you'll find a link to their
>> support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
>> .  Download it (something like "MoEx-1_0-st-v1 Probe Sequences,
>> tabular format (130 MB, 3/19/08)") and place it in
>> annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is
>> correct by trying the following:
>>
>> > library("aroma.affymetrix");
>> > ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
>> > ptf
>> AffymetrixProbeTabFile:
>> Name: MoEx-1_0-st-v1
>> Tags:
>> Full name: MoEx-1_0-st-v1
>> Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab
>> File size: 460.47 MB (482839635 bytes)
>> RAM: 0.01 MB
>> Number of data rows: NA
>> Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
>> 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
>> 'targetStrandedness', 'category'
>> Number of text lines: NA
>> AffymetrixCdfFile:
>> Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> Filename: MoEx-1_0-st-v1.cdf
>> Filesize: 274.30MB
>> Chip type: MoEx-1_0-st-v1
>> RAM: 0.00MB
>> File format: v4 (binary; XDA)
>> Dimension: 2560x2560
>> Number of cells: 6553600
>> Number of units: 1257006
>> Cells per unit: 5.21
>> Number of QC units: 0
>>
>> If you get that to work, then your script should work.
>>
>> Let me now if this solved your problem.
>>
>> /Henrik
>>
>> On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee
>> <[hidden email]> wrote:
>> > Respected Dr Bengtsson,
>> > My codes and outputs are as follows:
>> >> source("http://aroma-project.org/hbLite.R");
>> >> hbInstall("aroma.affymetrix")
>> >> source("http://aroma-project.org/hbLite.R");
>> >> hbInstall("aroma.cn")
>> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> dataSet <- "Exon Data"
>> >> chipType <- "MoEx-1_0-st-v1"
>> >> cdf <-
>> >> AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> >> print(cdf)
>> > AffymetrixCdfFile:
>> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> > Filesize: 30.53MB
>> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> > RAM: 0.00MB
>> > File format: v4 (binary; XDA)
>> > Dimension: 2560x2560
>> > Number of cells: 6553600
>> > Number of units: 17831
>> > Cells per unit: 367.54
>> > Number of QC units: 1
>> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >> print(csR)
>> > AffymetrixCelSet:
>> > Name: Exon Data
>> > Tags:
>> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> > Platform: Affymetrix
>> > Chip type: MoEx-1_0-st-v1
>> > Number of arrays: 7
>> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> > Total file size: 440.55MB
>> > RAM: 0.01MB
>> >> cdf <- getCdf(csR)
>> >> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>> >> setCdf(csR, cdfS)
>> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >> print(bc)
>> > GcRmaBackgroundCorrection:
>> > Data set: Exon Data
>> > Input tags:
>> > User tags: *
>> > Asterisk ('*') tags: GRBC
>> > Output tags: GRBC
>> > Number of files: 7 (440.55MB)
>> > Platform: Affymetrix
>> > Chip type: MoEx-1_0-st-v1
>> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
>> > indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
>> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> > Is done: FALSE
>> > RAM: 0.00MB
>> >> csB <- process(bc, verbose=verbose)
>> > 20100927 16:31:40|Background correcting data set...
>> > 20100927 16:31:40| Computing probe affinities...
>> > 20100927 16:31:40|  Computing GCRMA probe affinities for 1257006
>> > units...
>> > 20100927 16:31:40|   Identify PMs and MMs among the CDF cell indices...
>> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >        Mode   FALSE    TRUE    NA's
>> >     logical  334476 4931683       0
>> > 20100927 16:33:30|    MMs are defined as non-PMs
>> > 20100927 16:33:30|    Number of PMs: 4931683
>> > 20100927 16:33:30|    Number of MMs: 334476
>> > 20100927 16:33:30|   Identify PMs and MMs among the CDF cell
>> > indices...done
>> > 20100927 16:33:30|   Reading probe-sequence data...
>> > 20100927 16:33:30|    Retrieving probe-sequence data...
>> > 20100927 16:33:30|     Chip type (full): MoEx-1_0-st-v1
>> > 20100927 16:33:30|     Locating probe-tab file...
>> > 20100927 16:33:30|      Chip type: MoEx-1_0-st-v1
>> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> > <environment>,
>> >  :
>> >
>> > [2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
>> > deprectated (v1) search rules:
>> >   at throw(Exception(...))
>> >   at throw.default("Found probe-tab file only by means of deprectated
>> > (v1
>> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> > search
>> >   at method(static, ...)
>> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>> >   at method(static, ...)
>> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> > les
>> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> > ver
>> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> > less(verbos
>> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> > Data,GRBC/
>> >   at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>> >   at do.call("bgAdjustGcrma", args = args)
>> >   at process.GcRmaBackgroundCorrection(
>> > 20100927 16:33:30|     Locating probe-tab file...done
>> > 20100927 16:33:30|    Retrieving probe-sequence data...done
>> > 20100927 16:33:30|   Reading probe-sequence data...done
>> > 20100927 16:33:30|  Computing GCRMA probe affinities for 1257006
>> > units...done
>> > 20100927 16:33:30| Computing probe affinities...done
>> > 20100927 16:33:30|Background correcting data set...done
>> >> traceback()
>> > 17: throw.Exception(Exception(...))
>> > 16: throw(Exception(...))
>> > 15: throw.default("Found probe-tab file only by means of deprectated
>> > (v1)
>> > search rules: ",
>> >         pathname)
>> > 14: throw("Found probe-tab file only by means of deprectated (v1) search
>> > rules: ",
>> >         pathname)
>> > 13: method(static, ...)
>> > 12: AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>> >         ...)
>> > 11: method(static, ...)
>> > 10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> > less(verbose,
>> >         100))
>> > 9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>> > verbose)
>> > 8: getProbeSequenceData(this, safe = safe, verbose = verbose)
>> > 7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> >        verbose = less(verbose))
>> > 6: computeAffinities(cdf, paths = probePath, ..., verbose =
>> > less(verbose))
>> > 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> > Data,GRBC/MoEx-1_0-st-v1",
>> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
>> > NULL,
>> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >        gsbParameters = NULL, .deprecated = FALSE)
>> > 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
>> > NULL,
>> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >        gsbParameters = NULL, .deprecated = FALSE)
>> > 3: do.call("bgAdjustGcrma", args = args)
>> > 2: process.GcRmaBackgroundCorrection(bc, verbose = verbose)
>> > 1: process(bc, verbose = verbose)
>> >> sessionInfo()
>> > R version 2.11.1 (2010-05-31)
>> > x86_64-apple-darwin9.8.0
>> > locale:
>> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> > attached base packages:
>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>> > other attached packages:
>> >  [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7        affxparser_1.20.0
>> >  [4] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>> >  [7] matrixStats_0.2.1      R.rsp_0.4.0            R.filesets_0.9.0
>> > [10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.2
>> > [13] R.oo_1.7.4             R.methodsS3_1.2.1
>> > loaded via a namespace (and not attached):
>> > [1] tools_2.11.1
>> > The working directory is desktop and the path for the cdf file and the
>> > raw
>> > data is as follows:
>> >
>> > /Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> > ( I have several other cdf files
>> >
>> > like MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
>> > and MoEx-1_0-st-v1.cdf in the same directory.)
>> > /Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/
>> > DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P2_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P3_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P6_(MoEx-1_0-st-v1).CEL
>> > DK Litter D15 P14_(MoEx-1_0-st-v1).CEL
>> > Moreover I am following the thread and implementing the code you
>> > suggested
>> > there but it is not working with my dataset. Please help.
>> > Thank you,
>> > Prithish Banerjee,
>> > Graduate Research Assistant,
>> > Department of Statistics,
>> > West Virginia University.
>> >
>> > On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson <[hidden email]>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> first of all, for this chip type you need to specify:
>> >>
>> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> >>
>> >> Moreover, you cannot use the custom CDF in the
>> >> GcRmaBackgroundCorrection step, and have to do the follow workaround
>> >> illustrated in the below example:
>> >>
>> >>
>> >> library("aroma.affymetrix");
>> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> dataSet <- "Affymetrix-Tissues";
>> >> chipType <- "MoEx-1_0-st-v1";
>> >>
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> # Setup data set
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> cdf <- AffymetrixCdfFile$byChipType(chipType,
>> >> tags="coreR1,A20080718,MR");
>> >> print(cdf);
>> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
>> >> print(csR);
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> # gcRMA-style background correction
>> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> # Currently, you must use the standard CDF file.
>> >> cdf <- getCdf(csR);
>> >> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
>> >> setCdf(csR, cdfS);
>> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> >> print(bc);
>> >> csB <- process(bc, verbose=verbose);
>> >> print(csB);
>> >> # Now, use the custom CDF in what follows
>> >> setCdf(csB, cdf);
>> >> print(csB);
>> >>
>> >> Yes, those last steps are rather confusing - we're working on updating
>> >> the code so you don't have to do that yourself.
>> >>
>> >> FYI, the above solution/workaround was resolved in thread 'GCRMA
>> >> normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
>> >> http://goo.gl/cniq.
>> >>
>> >> Hope this helps
>> >>
>> >> /Henrik
>> >>
>> >> On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
>> >> <[hidden email]> wrote:
>> >> > Hi All,
>> >> > I am trying to normalize a mouse exon array dataset using GCRMA
>> >> > normalization technique. I have exactly followed all the necessary
>> >> > steps
>> >> > for
>> >> > storing the dataset and the cdf file. the code and the output I am
>> >> > using
>> >> > are
>> >> > as follows:
>> >> >
>> >> > source("http://aroma-project.org/hbLite.R");
>> >> >
>> >> > hbInstall("aroma.affymetrix")
>> >> >
>> >> > source("http://aroma-project.org/hbLite.R");
>> >> >
>> >> > hbInstall("aroma.cn")
>> >> >
>> >> > verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> >
>> >> > dataSet <- "Exon Data" [the path in the working directory is
>> >> > rawData/Exon
>> >> > Data/MoEx-1_0-st-v1/*.CEL files]
>> >> >
>> >> > chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
>> >> >
>> >> >
>> >> > annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>> >> >
>> >> > cdf <-
>> >> > AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> >> > [converted to binary using convertCdf command]
>> >> >
>> >> > print(cdf)
>> >> >
>> >> > AffymetrixCdfFile:
>> >> >
>> >> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> >> >
>> >> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> >> >
>> >> > Filesize: 30.53MB
>> >> >
>> >> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> >> >
>> >> > RAM: 0.00MB
>> >> >
>> >> > File format: v4 (binary; XDA)
>> >> >
>> >> > Dimension: 2560x2560
>> >> >
>> >> > Number of cells: 6553600
>> >> >
>> >> > Number of units: 17831
>> >> >
>> >> > Cells per unit: 367.54
>> >> >
>> >> > Number of QC units: 1
>> >> >
>> >> > csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >> >
>> >> > print(csR)
>> >> >
>> >> > AffymetrixCelSet:
>> >> >
>> >> > Name: Exon Data
>> >> >
>> >> > Tags:
>> >> >
>> >> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> >> >
>> >> > Platform: Affymetrix
>> >> >
>> >> > Chip type: MoEx-1_0-st-v1
>> >> >
>> >> > Number of arrays: 7
>> >> >
>> >> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> >> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> >> >
>> >> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> >> >
>> >> > Total file size: 440.55MB
>> >> >
>> >> > RAM: 0.01MB
>> >> >
>> >> > cdf <- getCdf(csR)
>> >> >
>> >> > cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf,
>> >> > fullname=FALSE))
>> >> >
>> >> > setCdf(csR, cdfS)
>> >> >
>> >> > bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >> >
>> >> > print(bc)
>> >> >
>> >> > GcRmaBackgroundCorrection:
>> >> >
>> >> > Data set: Exon Data
>> >> >
>> >> > Input tags:
>> >> >
>> >> > User tags: *
>> >> >
>> >> > Asterisk ('*') tags: GRBC
>> >> >
>> >> > Output tags: GRBC
>> >> >
>> >> > Number of files: 7 (440.55MB)
>> >> >
>> >> > Platform: Affymetrix
>> >> >
>> >> > Chip type: MoEx-1_0-st-v1
>> >> >
>> >> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
>> >> > indicesNegativeControl: NULL, affinities: NULL, type: chr
>> >> > "affinities",
>> >> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>> >> >
>> >> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> >> >
>> >> > Is done: FALSE
>> >> >
>> >> > RAM: 0.00MB
>> >> >
>> >> > csB <- process(bc, verbose=verbose)
>> >> >
>> >> > 20100923 13:24:12|Background correcting data set...
>> >> >
>> >> > 20100923 13:24:12| Computing probe affinities...
>> >> >
>> >> > 20100923 13:24:12|  Computing GCRMA probe affinities for 1257006
>> >> > units...
>> >> >
>> >> > 20100923 13:24:12|   Identify PMs and MMs among the CDF cell
>> >> > indices...
>> >> >
>> >> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >> >
>> >> >        Mode   FALSE    TRUE    NA's
>> >> >
>> >> >     logical  334476 4931683       0
>> >> >
>> >> > 20100923 13:25:57|    MMs are defined as non-PMs
>> >> >
>> >> > 20100923 13:25:57|    Number of PMs: 4931683
>> >> >
>> >> > 20100923 13:25:57|    Number of MMs: 334476
>> >> >
>> >> > 20100923 13:25:57|   Identify PMs and MMs among the CDF cell
>> >> > indices...done
>> >> >
>> >> > 20100923 13:25:57|   Reading probe-sequence data...
>> >> >
>> >> > 20100923 13:25:57|    Retrieving probe-sequence data...
>> >> >
>> >> > 20100923 13:25:57|     Chip type (full): MoEx-1_0-st-v1
>> >> >
>> >> > 20100923 13:25:57|     Locating probe-tab file...
>> >> >
>> >> > 20100923 13:25:57|      Chip type: MoEx-1_0-st-v1
>> >> >
>> >> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> >> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> >> > <environment>,
>> >> >  :
>> >> >
>> >> >
>> >> >
>> >> > [2010-09-23 13:25:57] Exception: Found probe-tab file only by means
>> >> > of
>> >> > deprectated (v1) search rules:
>> >> >
>> >> >   at throw(Exception(...))
>> >> >
>> >> >   at throw.default("Found probe-tab file only by means of deprectated
>> >> > (v1
>> >> >
>> >> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> >> > search
>> >> >
>> >> >   at method(static, ...)
>> >> >
>> >> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>> >> > ...)
>> >> >
>> >> >   at method(static, ...)
>> >> >
>> >> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> >> > les
>> >> >
>> >> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe,
>> >> > verbose =
>> >> >
>> >> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >> >
>> >> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> >> > ver
>> >> >
>> >> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> >> > less(verbos
>> >> >
>> >> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> >> > Data,GRBC/
>> >> >
>> >> >   at bgAdjustGcrma(NA, path = "probeData/Exon
>> >> > Data,GRBC/MoEx-1_0-st-v1",
>> >> >
>> >> >   at do.call("bgAdjustGcrma", args = args)
>> >> >
>> >> >   at process.GcRmaBackgroundCorrection(
>> >> >
>> >> > 20100923 13:25:57|     Locating probe-tab file...done
>> >> >
>> >> > 20100923 13:25:57|    Retrieving probe-sequence data...done
>> >> >
>> >> > 20100923 13:25:57|   Reading probe-sequence data...done
>> >> >
>> >> > 20100923 13:25:57|  Computing GCRMA probe affinities for 1257006
>> >> > units...done
>> >> >
>> >> > 20100923 13:25:57| Computing probe affinities...done
>> >> >
>> >> > 20100923 13:25:57|Background correcting data set...done
>> >> >
>> >> > Could anyone please enlighten me with the type of the error? I will
>> >> > be
>> >> > highly obliged if anyone please help me with this problem.
>> >> >
>> >> > Thank you.
>> >> >
>> >> > Prithish Banerjee.
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> > latest
>> >> > version of the package, 2) to report the output of sessionInfo() and
>> >> > traceback(), and 3) to post a complete code example.
>> >> >
>> >> >
>> >> > You received this message because you are subscribed to the Google
>> >> > Groups
>> >> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> >> > To post to this group, send email to
>> >> > [hidden email]
>> >> > To unsubscribe and other options, go to
>> >> > http://www.aroma-project.org/forum/
>> >> >
>> >>
>> >> --
>> >> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> latest version of the package, 2) to report the output of sessionInfo()
>> >> and
>> >> traceback(), and 3) to post a complete code example.
>> >>
>> >>
>> >> You received this message because you are subscribed to the Google
>> >> Groups
>> >> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> >> To post to this group, send email to [hidden email]
>> >> To unsubscribe and other options, go to
>> >> http://www.aroma-project.org/forum/
>> >
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
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Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Henrik Bengtsson-4
Hi.

On Wed, Oct 20, 2010 at 2:47 PM, Prithish Banerjee
<[hidden email]> wrote:
> Respected Dr Bengtsson,
> Thank you for your help. I was working with the human-exon dataset and found
> that all the probe sequence tabular files are in ASCII format( from
> affymetrix). Is it possible to convert the ptf files to binary same as the
> cdf files??

So, as part of generalizing the aroma framework to support more chip
types, I did indeed went ahead an imported the sequence information in
the Affymetrix probe tab files into a so called Aroma Cell Sequence
(ACS) file, cf.

"MoEx-1_0-st-v1,HB20100926.acs - Aroma Cell Sequence (ACS) annotation
file mapping cell indices to 25-mer sequences and target strandness.
Sources: Affymetrix probe_tab file.  The latter provides only
4,779,314 (72.9%) out of 6,553,600 sequences; please help us find the
sequences for the remaining probes.  Created by: Henrik Bengtsson,
2010-09-26."

URL: http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1

However, as you see from my note there, the sequence information
provided by Affymetrix only covers 72.9% of the probes on the array.
For the remaining 17.1% of the probes we lack sequence information and
that *may* cause stability issue when estimating the GCRMA sequence
model parameters.  If you could prompt the Affymetrix support for more
sequence information on this chip type, that would be useful.

FYI, I've also done more generalization.  Bare with me (because it is
too complicated to give you early access to all of this already now),
but in the next release you will have access to:

o Now doGCRMA() automagically makes sure that the default CDF is used
  in the QuantileNormalization step, while use a custom CDF everywhere
  else if set.  Added argument 'type' to doGCRMA() which is passed to
  QuantileNormalization().
o GENERALIZATION: Now GcRmaBackgroundCorrection(..., type="affinities")
  can process also chip types for which there are no MMs and for
  which non-specific probes are explicitly specified.
o GENERALIZATION: Now GcRmaBackgroundCorrection calculates gcRMA probe
  affinites based on Aroma Cell Sequence (ACS) annotation files.
  For backward compatibility, it turns to Affymetrix probe-tab files
  if an ACS file is not located.

/Henrik

> Thank you,
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> On Wed, Sep 29, 2010 at 3:14 PM, Henrik Bengtsson <[hidden email]>
> wrote:
>>
>> Hi.
>>
>> On Wed, Sep 29, 2010 at 10:32 AM, Prithish Banerjee
>> <[hidden email]> wrote:
>> > Respected Dr Bengtsson,
>> > Thank you for the help. I have done what you have suggested and the
>> > following output is as follows:
>> >
>> > source("http://aroma-project.org/hbLite.R");
>> >
>> > hbInstall("aroma.affymetrix")
>> >
>> > source("http://aroma-project.org/hbLite.R");
>> >
>> > hbInstall("aroma.cn")
>> >
>> > verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >
>> > dataSet <- "Exon Data"
>> >
>> > chipType <- "MoEx-1_0-st-v1"
>> >
>> > cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> >
>> > print(cdf)
>> >
>> > ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
>> >
>> > print(ptf)
>> >
>> > csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >
>> > print(csR)
>> >
>> > cdf <- getCdf(csR)
>> >
>> > cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>> >
>> > setCdf(csR, cdfS)
>> >
>> > bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >
>> > print(bc)
>> >
>> > csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
>> > 20100928 22:40:59|Background correcting data set...
>> > 20100928 22:41:09| Computing probe affinities...
>> > 20100928 22:41:09|  Reading saved affinities: probeData/Exon
>> > Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...
>> > 20100928 22:41:10|  Reading saved affinities: probeData/Exon
>> > Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...done
>> > 20100928 22:41:10|  RAM: 50.00MB
>> > 20100928 22:41:10| Computing probe affinities...done
>> > 20100928 22:41:10| Background correcting data set...
>> > 20100928 22:41:16|  Already background corrected for "optical" effects
>> > 20100928 22:41:16| Background correcting data set...done
>> > 20100928 22:41:16| Estimating specific binding parameters...
>> > 20100928 22:41:16|  Extracting PM indices...
>> > 20100928 22:41:16|   Reading cell indices from CDF file...
>> > 20100928 22:41:16|    Pathname:
>> > annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf
>> > 20100928 22:41:16|    Units:
>> >      NULL
>> > 20100928 22:41:16|    lapplyInChunks()...
>> > 20100928 22:41:16|     Number of elements per chunk: 1e+05
>> > 20100928 22:41:16|     Chunk #1 of 13...
>> > 20100928 22:41:16|      Elements:
>> >        int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20100928 22:41:16|      Querying CDF file...
>> > 20100928 22:41:20|      Querying CDF file...done
>> > 20100928 22:41:21|      Restructuring...
>> > 20100928 22:41:21|      Restructuring...done
>> >                  used (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058626  110    6907341 368.9  17756025 948.3
>> >       Vcells 14800385  113   55506200 423.5 106800686 814.9
>> > 20100928 22:41:21|     Chunk #1 of 13...done
>> > 20100928 22:41:21|     Chunk #2 of 13...
>> > 20100928 22:41:21|      Elements:
>> >        int [1:100000] 100001 100002 100003 100004 100005 100006 100007
>> > 100008 100009 100010 ...
>> > 20100928 22:41:21|      Querying CDF file...
>> > 20100928 22:41:25|      Querying CDF file...done
>> > 20100928 22:41:26|      Restructuring...
>> > 20100928 22:41:26|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058632 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 14946933 114.1   44404960 338.8 106800686 814.9
>> > 20100928 22:41:26|     Chunk #2 of 13...done
>> > 20100928 22:41:26|     Chunk #3 of 13...
>> > 20100928 22:41:26|      Elements:
>> >        int [1:100000] 200001 200002 200003 200004 200005 200006 200007
>> > 200008 200009 200010 ...
>> > 20100928 22:41:26|      Querying CDF file...
>> > 20100928 22:41:30|      Querying CDF file...done
>> > 20100928 22:41:30|      Restructuring...
>> > 20100928 22:41:30|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058634 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 15101344 115.3   44404960 338.8 106800686 814.9
>> > 20100928 22:41:31|     Chunk #3 of 13...done
>> > 20100928 22:41:31|     Chunk #4 of 13...
>> > 20100928 22:41:31|      Elements:
>> >        int [1:100000] 300001 300002 300003 300004 300005 300006 300007
>> > 300008 300009 300010 ...
>> > 20100928 22:41:31|      Querying CDF file...
>> > 20100928 22:41:35|      Querying CDF file...done
>> > 20100928 22:41:35|      Restructuring...
>> > 20100928 22:41:35|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058634 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 15249056 116.4   44404960 338.8 106800686 814.9
>> > 20100928 22:41:36|     Chunk #4 of 13...done
>> > 20100928 22:41:36|     Chunk #5 of 13...
>> > 20100928 22:41:36|      Elements:
>> >        int [1:100000] 400001 400002 400003 400004 400005 400006 400007
>> > 400008 400009 400010 ...
>> > 20100928 22:41:36|      Querying CDF file...
>> > 20100928 22:41:40|      Querying CDF file...done
>> > 20100928 22:41:40|      Restructuring...
>> > 20100928 22:41:40|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058635 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 15397125 117.5   44404960 338.8 106800686 814.9
>> > 20100928 22:41:40|     Chunk #5 of 13...done
>> > 20100928 22:41:40|     Chunk #6 of 13...
>> > 20100928 22:41:40|      Elements:
>> >        int [1:100000] 500001 500002 500003 500004 500005 500006 500007
>> > 500008 500009 500010 ...
>> > 20100928 22:41:40|      Querying CDF file...
>> > 20100928 22:41:44|      Querying CDF file...done
>> > 20100928 22:41:45|      Restructuring...
>> > 20100928 22:41:45|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058637 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 15541779 118.6   44404960 338.8 106800686 814.9
>> > 20100928 22:41:45|     Chunk #6 of 13...done
>> > 20100928 22:41:45|     Chunk #7 of 13...
>> > 20100928 22:41:45|      Elements:
>> >        int [1:100000] 600001 600002 600003 600004 600005 600006 600007
>> > 600008 600009 600010 ...
>> > 20100928 22:41:45|      Querying CDF file...
>> > 20100928 22:41:49|      Querying CDF file...done
>> > 20100928 22:41:50|      Restructuring...
>> > 20100928 22:41:50|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058637 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 15690489 119.8   44404960 338.8 106800686 814.9
>> > 20100928 22:41:50|     Chunk #7 of 13...done
>> > 20100928 22:41:50|     Chunk #8 of 13...
>> > 20100928 22:41:50|      Elements:
>> >        int [1:100000] 700001 700002 700003 700004 700005 700006 700007
>> > 700008 700009 700010 ...
>> > 20100928 22:41:50|      Querying CDF file...
>> > 20100928 22:41:54|      Querying CDF file...done
>> > 20100928 22:41:54|      Restructuring...
>> > 20100928 22:41:54|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058638 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 15837280 120.9   44404960 338.8 106800686 814.9
>> > 20100928 22:41:55|     Chunk #8 of 13...done
>> > 20100928 22:41:55|     Chunk #9 of 13...
>> > 20100928 22:41:55|      Elements:
>> >        int [1:100000] 800001 800002 800003 800004 800005 800006 800007
>> > 800008 800009 800010 ...
>> > 20100928 22:41:55|      Querying CDF file...
>> > 20100928 22:41:59|      Querying CDF file...done
>> > 20100928 22:41:59|      Restructuring...
>> > 20100928 22:41:59|      Restructuring...done
>> >                  used (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058640  110    6907341 368.9  17756025 948.3
>> >       Vcells 15987604  122   44404960 338.8 106800686 814.9
>> > 20100928 22:41:59|     Chunk #9 of 13...done
>> > 20100928 22:41:59|     Chunk #10 of 13...
>> > 20100928 22:41:59|      Elements:
>> >        int [1:100000] 900001 900002 900003 900004 900005 900006 900007
>> > 900008 900009 900010 ...
>> > 20100928 22:41:59|      Querying CDF file...
>> > 20100928 22:42:04|      Querying CDF file...done
>> > 20100928 22:42:04|      Restructuring...
>> > 20100928 22:42:04|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2066219 110.4    6907341 368.9  17756025 948.3
>> >       Vcells 16292565 124.4   44404960 338.8 106800686 814.9
>> > 20100928 22:42:04|     Chunk #10 of 13...done
>> > 20100928 22:42:04|     Chunk #11 of 13...
>> > 20100928 22:42:04|      Elements:
>> >        int [1:100000] 1000001 1000002 1000003 1000004 1000005 1000006
>> > 1000007 1000008 1000009 1000010 ...
>> > 20100928 22:42:05|      Querying CDF file...
>> > 20100928 22:42:08|      Querying CDF file...done
>> > 20100928 22:42:09|      Restructuring...
>> > 20100928 22:42:09|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058641 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 16431821 125.4   44404960 338.8 106800686 814.9
>> > 20100928 22:42:09|     Chunk #11 of 13...done
>> > 20100928 22:42:09|     Chunk #12 of 13...
>> > 20100928 22:42:09|      Elements:
>> >        int [1:100000] 1100001 1100002 1100003 1100004 1100005 1100006
>> > 1100007 1100008 1100009 1100010 ...
>> > 20100928 22:42:09|      Querying CDF file...
>> > 20100928 22:42:13|      Querying CDF file...done
>> > 20100928 22:42:14|      Restructuring...
>> > 20100928 22:42:14|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  2058642 110.0    6907341 368.9  17756025 948.3
>> >       Vcells 16577525 126.5   44404960 338.8 106800686 814.9
>> > 20100928 22:42:14|     Chunk #12 of 13...done
>> > 20100928 22:42:14|     Chunk #13 of 13...
>> > 20100928 22:42:14|      Elements:
>> >        int [1:57006] 1200001 1200002 1200003 1200004 1200005 1200006
>> > 1200007
>> > 1200008 1200009 1200010 ...
>> > 20100928 22:42:14|      Querying CDF file...
>> > 20100928 22:42:16|      Querying CDF file...done
>> > 20100928 22:42:17|      Restructuring...
>> > 20100928 22:42:17|      Restructuring...done
>> >                  used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >       Ncells  1671697  89.3    5525872 295.2  17756025 948.3
>> >       Vcells 16271204 124.2   44404960 338.8 106800686 814.9
>> > 20100928 22:42:17|     Chunk #13 of 13...done
>> > 20100928 22:42:17|    lapplyInChunks()...done
>> > 20100928 22:42:17|   Reading cell indices from CDF file...done
>> >               used  (Mb) gc trigger  (Mb)  max used  (Mb)
>> >    Ncells  1158492  61.9    4420697 236.1  17756025 948.3
>> >    Vcells 13870500 105.9   44404960 338.8 106800686 814.9
>> > 20100928 22:42:17|   readUnits.AffymetrixCdfFile(): Updating cache
>> > 20100928 22:43:21|  Extracting PM indices...done
>> >              used (Mb) gc trigger  (Mb)  max used  (Mb)
>> >   Ncells  1158442 61.9    6163167 329.2  17756025 948.3
>> >   Vcells 11250131 85.9   35523968 271.1 106800686 814.9
>> > 20100928 22:43:22|  Extracting 25000 random PM intensities across CEL
>> > set...
>> > 20100928 22:43:22|   Array #1 of 7...
>> > 20100928 22:43:22|   Array #1 of 7...done
>> > 20100928 22:43:22|   Array #2 of 7...
>> > 20100928 22:43:23|   Array #2 of 7...done
>> > 20100928 22:43:23|   Array #3 of 7...
>> > 20100928 22:43:24|   Array #3 of 7...done
>> > 20100928 22:43:24|   Array #4 of 7...
>> > 20100928 22:43:26|   Array #4 of 7...done
>> > 20100928 22:43:26|   Array #5 of 7...
>> > 20100928 22:43:27|   Array #5 of 7...done
>> > 20100928 22:43:27|   Array #6 of 7...
>> > 20100928 22:43:28|   Array #6 of 7...done
>> > 20100928 22:43:28|   Array #7 of 7...
>> > 20100928 22:43:30|   Array #7 of 7...done
>> >               used (Mb) gc trigger  (Mb)  max used  (Mb)
>> >    Ncells  1158299 61.9    4930533 263.4  17756025 948.3
>> >    Vcells 11274772 86.1   35523968 271.1 106800686 814.9
>> > 20100928 22:43:31|  Extracting 25000 random PM intensities across CEL
>> > set...done
>> > 20100928 22:43:31|  Extracting probe affinities and fitting linear
>> > model...
>> >               used (Mb) gc trigger  (Mb)  max used  (Mb)
>> >    Ncells  1158298 61.9    3944426 210.7  17756025 948.3
>> >    Vcells 11287264 86.2   35523968 271.1 106800686 814.9
>> > 20100928 22:43:32|   Fitting the GCRMA background linear model...
>> >      num [1:25000] 5.39 8.46 8.41 6.89 8.05 ...
>> >      num [1:25000] 0.485 -0.764 1.766 -0.857 0.344 ...
>> >
>> >     Call:
>> >     lm(formula = pm.random2 ~ aff)
>> >
>> >     Coefficients:
>> >     (Intercept)          aff
>> >          6.5646       0.4193
>> >
>> > 20100928 22:43:32|   Fitting the GCRMA background linear model...done
>> > 20100928 22:43:32|  Extracting probe affinities and fitting linear
>> > model...done
>> > 20100928 22:43:32| Estimating specific binding parameters...done
>> > 20100928 22:43:32| Adjusting 7 arrays...
>> > 20100928 22:43:32|  Array #1 of 7...
>> >    AffymetrixCelFile:
>> >    Name: DK Litter D15 P1_(MoEx-1_0-st-v1)
>> >    Tags:
>> >    Full name: DK Litter D15 P1_(MoEx-1_0-st-v1)
>> >    Pathname: probeData/Exon Data,OBC/MoEx-1_0-st-v1/DK Litter D15
>> > P1_(MoEx-1_0-st-v1).CEL
>> >    File size: 62.50 MB (65536703 bytes)
>> >    RAM: 0.00 MB
>> >    File format: v4 (binary; XDA)
>> >    Platform: Affymetrix
>> >    Chip type: MoEx-1_0-st-v1
>> >    Timestamp: 2010-09-28 14:26:37
>> > 20100928 22:43:32|   Obtaining PM and MM signals and affinities...
>> > 20100928 22:45:16|   Obtaining PM and MM signals and affinities...done
>> > 20100928 22:45:16|   Estimating non-specific binding parameters...
>> > Error in quantile.default(a1, 0.001) :
>> >   missing values and NaN's not allowed if 'na.rm' is FALSE
>> > 20100928 22:45:16|  Array #1 of 7...done
>> > 20100928 22:45:16| Adjusting 7 arrays...done
>> > 20100928 22:45:16|Background correcting data set...done
>> >> traceback()
>> > 15: stop("missing values and NaN's not allowed if 'na.rm' is FALSE")
>> > 14: quantile.default(a1, 0.001)
>> > 13: quantile(a1, 0.001)
>> > 12: seq(quantile(a1, 0.001), quantile(a1, 0.999), len = 26)
>> > 11: cut.default(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1,
>> >         0.999), len = 26), Inf))
>> > 10: cut(a1, c(-Inf, seq(quantile(a1, 0.001), quantile(a1, 0.999),
>> >         len = 26), Inf))
>> > 9: bg.parameters.ns(ncs[index.affinities], anc, apm)
>> > 8: gcrma::bg.adjust.affinities(pm, mm, apm, amm, index.affinities =
>> > 1:length(pm),
>> >        k = k, fast = fast)
>> > 7: bgAdjustGcrma.AffymetrixCelFile(df, path = path, type = type,
>> >        indicesNegativeControl = indicesNegativeControl, affinities =
>> > affinities,
>> >        gsbAdjust = gsbAdjust, parametersGsb = parametersGsb, k = k,
>> >        rho = rho, stretch = stretch, fast = fast, overwrite = overwrite,
>> >        skip = skip, ..., verbose = less(verbose), .deprecated =
>> > .deprecated)
>> > 6: bgAdjustGcrma(df, path = path, type = type, indicesNegativeControl =
>> > indicesNegativeControl,
>> >        affinities = affinities, gsbAdjust = gsbAdjust, parametersGsb =
>> > parametersGsb,
>> >        k = k, rho = rho, stretch = stretch, fast = fast, overwrite =
>> > overwrite,
>> >        skip = skip, ..., verbose = less(verbose), .deprecated =
>> > .deprecated)
>> > 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> > Data,GRBC/MoEx-1_0-st-v1",
>> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
>> > NULL,
>> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >        gsbParameters = NULL, .deprecated = FALSE)
>> > 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >        typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
>> > NULL,
>> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >        gsbParameters = NULL, .deprecated = FALSE)
>> > 3: do.call("bgAdjustGcrma", args = args)
>> > 2: process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose =
>> > verbose,
>> >        na.rm = "TRUE")
>> > 1: process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
>> >
>> > Is it somehow  possible to replace the NaN and missing values to some
>> > other
>> > value (like the mean or median or some small number close to 0)?
>>
>> It is good that we made progress.  The new error looks like a "bug" in
>> the sense that that piece of code does not expect NAs to appear.  I
>> have to looking into this and figure out if NAs can indeed be expected
>> of if they are incorrectly introduced earlier in the pipeline or not.
>>  I will also go back to our redundancy tests and check, because we do
>> not detect this problem there.  If NAs should be allowed, the fix
>> should be simple, but has to be done by me updating the code.
>>
>> I'll get back to your when I've done this.
>>
>> > Also I am getting some output in the probeData folder as:
>> > probeData/Exon Data,OBC/MoEx-1_0-st-v1/(all the *.cel files) and
>> > probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa.
>> > What are this outputs corresponds to?
>>
>> That file contains the GCRMA probe affinities computed from the CDF
>> and the probe-sequence file.  Consider it as an internal file that is
>> saved to disk so that the next time you run the pipeline, if redone,
>> it be found and the processing will be much faster.
>>
>> Sorry about all these issues.  As I almost write in every
>> correspondence related to gcRMA processing - the inner code was
>> written in the early days and specifically for a few chip types.
>> After that new chip types came around and things became a bit shaky.
>> However and although not really visible to the end user, we are slowly
>> updating the code and moving to a more robust and generic solution.
>> What the end user probably sees is more and more informative error
>> messages.  So, base with us.
>>
>> Cheers,
>>
>> Henrik
>>
>> > Again thank you for the help.
>> > Prithish Banerjee,
>> > Graduate Research Assistant,
>> > Department of Statistics,
>> > West Virginia University.
>> >
>> > On Tue, Sep 28, 2010 at 1:47 AM, Henrik Bengtsson <[hidden email]>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> sorry, my mistake.  I missed that you already did this.
>> >>
>> >> You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
>> >> You can download it from Affymetrix and you'll find a link to their
>> >> support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
>> >> .  Download it (something like "MoEx-1_0-st-v1 Probe Sequences,
>> >> tabular format (130 MB, 3/19/08)") and place it in
>> >> annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is
>> >> correct by trying the following:
>> >>
>> >> > library("aroma.affymetrix");
>> >> > ptf <- AffymetrixProbeTabFile$byChipType("MoEx-1_0-st-v1");
>> >> > ptf
>> >> AffymetrixProbeTabFile:
>> >> Name: MoEx-1_0-st-v1
>> >> Tags:
>> >> Full name: MoEx-1_0-st-v1
>> >> Pathname:
>> >> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab
>> >> File size: 460.47 MB (482839635 bytes)
>> >> RAM: 0.01 MB
>> >> Number of data rows: NA
>> >> Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
>> >> 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
>> >> 'targetStrandedness', 'category'
>> >> Number of text lines: NA
>> >> AffymetrixCdfFile:
>> >> Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> >> Filename: MoEx-1_0-st-v1.cdf
>> >> Filesize: 274.30MB
>> >> Chip type: MoEx-1_0-st-v1
>> >> RAM: 0.00MB
>> >> File format: v4 (binary; XDA)
>> >> Dimension: 2560x2560
>> >> Number of cells: 6553600
>> >> Number of units: 1257006
>> >> Cells per unit: 5.21
>> >> Number of QC units: 0
>> >>
>> >> If you get that to work, then your script should work.
>> >>
>> >> Let me now if this solved your problem.
>> >>
>> >> /Henrik
>> >>
>> >> On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee
>> >> <[hidden email]> wrote:
>> >> > Respected Dr Bengtsson,
>> >> > My codes and outputs are as follows:
>> >> >> source("http://aroma-project.org/hbLite.R");
>> >> >> hbInstall("aroma.affymetrix")
>> >> >> source("http://aroma-project.org/hbLite.R");
>> >> >> hbInstall("aroma.cn")
>> >> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> >> dataSet <- "Exon Data"
>> >> >> chipType <- "MoEx-1_0-st-v1"
>> >> >> cdf <-
>> >> >> AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> >> >> print(cdf)
>> >> > AffymetrixCdfFile:
>> >> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> >> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> >> > Filesize: 30.53MB
>> >> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> >> > RAM: 0.00MB
>> >> > File format: v4 (binary; XDA)
>> >> > Dimension: 2560x2560
>> >> > Number of cells: 6553600
>> >> > Number of units: 17831
>> >> > Cells per unit: 367.54
>> >> > Number of QC units: 1
>> >> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >> >> print(csR)
>> >> > AffymetrixCelSet:
>> >> > Name: Exon Data
>> >> > Tags:
>> >> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> >> > Platform: Affymetrix
>> >> > Chip type: MoEx-1_0-st-v1
>> >> > Number of arrays: 7
>> >> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> >> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> >> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> >> > Total file size: 440.55MB
>> >> > RAM: 0.01MB
>> >> >> cdf <- getCdf(csR)
>> >> >> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf,
>> >> >> fullname=FALSE))
>> >> >> setCdf(csR, cdfS)
>> >> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >> >> print(bc)
>> >> > GcRmaBackgroundCorrection:
>> >> > Data set: Exon Data
>> >> > Input tags:
>> >> > User tags: *
>> >> > Asterisk ('*') tags: GRBC
>> >> > Output tags: GRBC
>> >> > Number of files: 7 (440.55MB)
>> >> > Platform: Affymetrix
>> >> > Chip type: MoEx-1_0-st-v1
>> >> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
>> >> > indicesNegativeControl: NULL, affinities: NULL, type: chr
>> >> > "affinities",
>> >> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>> >> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> >> > Is done: FALSE
>> >> > RAM: 0.00MB
>> >> >> csB <- process(bc, verbose=verbose)
>> >> > 20100927 16:31:40|Background correcting data set...
>> >> > 20100927 16:31:40| Computing probe affinities...
>> >> > 20100927 16:31:40|  Computing GCRMA probe affinities for 1257006
>> >> > units...
>> >> > 20100927 16:31:40|   Identify PMs and MMs among the CDF cell
>> >> > indices...
>> >> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >> >        Mode   FALSE    TRUE    NA's
>> >> >     logical  334476 4931683       0
>> >> > 20100927 16:33:30|    MMs are defined as non-PMs
>> >> > 20100927 16:33:30|    Number of PMs: 4931683
>> >> > 20100927 16:33:30|    Number of MMs: 334476
>> >> > 20100927 16:33:30|   Identify PMs and MMs among the CDF cell
>> >> > indices...done
>> >> > 20100927 16:33:30|   Reading probe-sequence data...
>> >> > 20100927 16:33:30|    Retrieving probe-sequence data...
>> >> > 20100927 16:33:30|     Chip type (full): MoEx-1_0-st-v1
>> >> > 20100927 16:33:30|     Locating probe-tab file...
>> >> > 20100927 16:33:30|      Chip type: MoEx-1_0-st-v1
>> >> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> >> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> >> > <environment>,
>> >> >  :
>> >> >
>> >> > [2010-09-27 16:33:30] Exception: Found probe-tab file only by means
>> >> > of
>> >> > deprectated (v1) search rules:
>> >> >   at throw(Exception(...))
>> >> >   at throw.default("Found probe-tab file only by means of deprectated
>> >> > (v1
>> >> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> >> > search
>> >> >   at method(static, ...)
>> >> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>> >> > ...)
>> >> >   at method(static, ...)
>> >> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> >> > les
>> >> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe,
>> >> > verbose =
>> >> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> >> > ver
>> >> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> >> > less(verbos
>> >> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> >> > Data,GRBC/
>> >> >   at bgAdjustGcrma(NA, path = "probeData/Exon
>> >> > Data,GRBC/MoEx-1_0-st-v1",
>> >> >   at do.call("bgAdjustGcrma", args = args)
>> >> >   at process.GcRmaBackgroundCorrection(
>> >> > 20100927 16:33:30|     Locating probe-tab file...done
>> >> > 20100927 16:33:30|    Retrieving probe-sequence data...done
>> >> > 20100927 16:33:30|   Reading probe-sequence data...done
>> >> > 20100927 16:33:30|  Computing GCRMA probe affinities for 1257006
>> >> > units...done
>> >> > 20100927 16:33:30| Computing probe affinities...done
>> >> > 20100927 16:33:30|Background correcting data set...done
>> >> >> traceback()
>> >> > 17: throw.Exception(Exception(...))
>> >> > 16: throw(Exception(...))
>> >> > 15: throw.default("Found probe-tab file only by means of deprectated
>> >> > (v1)
>> >> > search rules: ",
>> >> >         pathname)
>> >> > 14: throw("Found probe-tab file only by means of deprectated (v1)
>> >> > search
>> >> > rules: ",
>> >> >         pathname)
>> >> > 13: method(static, ...)
>> >> > 12: AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>> >> >         ...)
>> >> > 11: method(static, ...)
>> >> > 10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
>> >> > less(verbose,
>> >> >         100))
>> >> > 9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose
>> >> > =
>> >> > verbose)
>> >> > 8: getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >> > 7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
>> >> >        verbose = less(verbose))
>> >> > 6: computeAffinities(cdf, paths = probePath, ..., verbose =
>> >> > less(verbose))
>> >> > 5: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> >> > Data,GRBC/MoEx-1_0-st-v1",
>> >> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >> >        typesToUpdate = "pm", indicesNegativeControl = NULL,
>> >> > affinities =
>> >> > NULL,
>> >> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >> >        gsbParameters = NULL, .deprecated = FALSE)
>> >> > 4: bgAdjustGcrma(NA, path = "probeData/Exon
>> >> > Data,GRBC/MoEx-1_0-st-v1",
>> >> >        verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> >> >        typesToUpdate = "pm", indicesNegativeControl = NULL,
>> >> > affinities =
>> >> > NULL,
>> >> >        type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
>> >> >        gsbParameters = NULL, .deprecated = FALSE)
>> >> > 3: do.call("bgAdjustGcrma", args = args)
>> >> > 2: process.GcRmaBackgroundCorrection(bc, verbose = verbose)
>> >> > 1: process(bc, verbose = verbose)
>> >> >> sessionInfo()
>> >> > R version 2.11.1 (2010-05-31)
>> >> > x86_64-apple-darwin9.8.0
>> >> > locale:
>> >> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> >> > attached base packages:
>> >> > [1] stats     graphics  grDevices utils     datasets  methods   base
>> >> > other attached packages:
>> >> >  [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7        affxparser_1.20.0
>> >> >  [4] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>> >> >  [7] matrixStats_0.2.1      R.rsp_0.4.0            R.filesets_0.9.0
>> >> > [10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.2
>> >> > [13] R.oo_1.7.4             R.methodsS3_1.2.1
>> >> > loaded via a namespace (and not attached):
>> >> > [1] tools_2.11.1
>> >> > The working directory is desktop and the path for the cdf file and
>> >> > the
>> >> > raw
>> >> > data is as follows:
>> >> >
>> >> >
>> >> > /Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> >> > ( I have several other cdf files
>> >> >
>> >> >
>> >> > like MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
>> >> > and MoEx-1_0-st-v1.cdf in the same directory.)
>> >> > /Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/
>> >> > DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
>> >> > DK Litter D15 P2_(MoEx-1_0-st-v1).CEL
>> >> > DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL
>> >> > DK Litter D15 P3_(MoEx-1_0-st-v1).CEL
>> >> > DK Litter D15 P6_(MoEx-1_0-st-v1).CEL
>> >> > DK Litter D15 P14_(MoEx-1_0-st-v1).CEL
>> >> > Moreover I am following the thread and implementing the code you
>> >> > suggested
>> >> > there but it is not working with my dataset. Please help.
>> >> > Thank you,
>> >> > Prithish Banerjee,
>> >> > Graduate Research Assistant,
>> >> > Department of Statistics,
>> >> > West Virginia University.
>> >> >
>> >> > On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> first of all, for this chip type you need to specify:
>> >> >>
>> >> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> >> >>
>> >> >> Moreover, you cannot use the custom CDF in the
>> >> >> GcRmaBackgroundCorrection step, and have to do the follow workaround
>> >> >> illustrated in the below example:
>> >> >>
>> >> >>
>> >> >> library("aroma.affymetrix");
>> >> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> >> dataSet <- "Affymetrix-Tissues";
>> >> >> chipType <- "MoEx-1_0-st-v1";
>> >> >>
>> >> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> >> # Setup data set
>> >> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> >> cdf <- AffymetrixCdfFile$byChipType(chipType,
>> >> >> tags="coreR1,A20080718,MR");
>> >> >> print(cdf);
>> >> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
>> >> >> print(csR);
>> >> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> >> # gcRMA-style background correction
>> >> >> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >> >> # Currently, you must use the standard CDF file.
>> >> >> cdf <- getCdf(csR);
>> >> >> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf,
>> >> >> fullname=FALSE));
>> >> >> setCdf(csR, cdfS);
>> >> >> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> >> >> print(bc);
>> >> >> csB <- process(bc, verbose=verbose);
>> >> >> print(csB);
>> >> >> # Now, use the custom CDF in what follows
>> >> >> setCdf(csB, cdf);
>> >> >> print(csB);
>> >> >>
>> >> >> Yes, those last steps are rather confusing - we're working on
>> >> >> updating
>> >> >> the code so you don't have to do that yourself.
>> >> >>
>> >> >> FYI, the above solution/workaround was resolved in thread 'GCRMA
>> >> >> normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
>> >> >> http://goo.gl/cniq.
>> >> >>
>> >> >> Hope this helps
>> >> >>
>> >> >> /Henrik
>> >> >>
>> >> >> On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
>> >> >> <[hidden email]> wrote:
>> >> >> > Hi All,
>> >> >> > I am trying to normalize a mouse exon array dataset using GCRMA
>> >> >> > normalization technique. I have exactly followed all the necessary
>> >> >> > steps
>> >> >> > for
>> >> >> > storing the dataset and the cdf file. the code and the output I am
>> >> >> > using
>> >> >> > are
>> >> >> > as follows:
>> >> >> >
>> >> >> > source("http://aroma-project.org/hbLite.R");
>> >> >> >
>> >> >> > hbInstall("aroma.affymetrix")
>> >> >> >
>> >> >> > source("http://aroma-project.org/hbLite.R");
>> >> >> >
>> >> >> > hbInstall("aroma.cn")
>> >> >> >
>> >> >> > verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> >> >
>> >> >> > dataSet <- "Exon Data" [the path in the working directory is
>> >> >> > rawData/Exon
>> >> >> > Data/MoEx-1_0-st-v1/*.CEL files]
>> >> >> >
>> >> >> > chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>> >> >> >
>> >> >> > cdf <-
>> >> >> > AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
>> >> >> > [converted to binary using convertCdf command]
>> >> >> >
>> >> >> > print(cdf)
>> >> >> >
>> >> >> > AffymetrixCdfFile:
>> >> >> >
>> >> >> > Path: annotationData/chipTypes/MoEx-1_0-st-v1
>> >> >> >
>> >> >> > Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>> >> >> >
>> >> >> > Filesize: 30.53MB
>> >> >> >
>> >> >> > Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>> >> >> >
>> >> >> > RAM: 0.00MB
>> >> >> >
>> >> >> > File format: v4 (binary; XDA)
>> >> >> >
>> >> >> > Dimension: 2560x2560
>> >> >> >
>> >> >> > Number of cells: 6553600
>> >> >> >
>> >> >> > Number of units: 17831
>> >> >> >
>> >> >> > Cells per unit: 367.54
>> >> >> >
>> >> >> > Number of QC units: 1
>> >> >> >
>> >> >> > csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>> >> >> >
>> >> >> > print(csR)
>> >> >> >
>> >> >> > AffymetrixCelSet:
>> >> >> >
>> >> >> > Name: Exon Data
>> >> >> >
>> >> >> > Tags:
>> >> >> >
>> >> >> > Path: rawData/Exon Data/MoEx-1_0-st-v1
>> >> >> >
>> >> >> > Platform: Affymetrix
>> >> >> >
>> >> >> > Chip type: MoEx-1_0-st-v1
>> >> >> >
>> >> >> > Number of arrays: 7
>> >> >> >
>> >> >> > Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
>> >> >> > P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>> >> >> >
>> >> >> > Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>> >> >> >
>> >> >> > Total file size: 440.55MB
>> >> >> >
>> >> >> > RAM: 0.01MB
>> >> >> >
>> >> >> > cdf <- getCdf(csR)
>> >> >> >
>> >> >> > cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf,
>> >> >> > fullname=FALSE))
>> >> >> >
>> >> >> > setCdf(csR, cdfS)
>> >> >> >
>> >> >> > bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>> >> >> >
>> >> >> > print(bc)
>> >> >> >
>> >> >> > GcRmaBackgroundCorrection:
>> >> >> >
>> >> >> > Data set: Exon Data
>> >> >> >
>> >> >> > Input tags:
>> >> >> >
>> >> >> > User tags: *
>> >> >> >
>> >> >> > Asterisk ('*') tags: GRBC
>> >> >> >
>> >> >> > Output tags: GRBC
>> >> >> >
>> >> >> > Number of files: 7 (440.55MB)
>> >> >> >
>> >> >> > Platform: Affymetrix
>> >> >> >
>> >> >> > Chip type: MoEx-1_0-st-v1
>> >> >> >
>> >> >> > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr
>> >> >> > "pm",
>> >> >> > indicesNegativeControl: NULL, affinities: NULL, type: chr
>> >> >> > "affinities",
>> >> >> > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters:
>> >> >> > NULL)
>> >> >> >
>> >> >> > Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>> >> >> >
>> >> >> > Is done: FALSE
>> >> >> >
>> >> >> > RAM: 0.00MB
>> >> >> >
>> >> >> > csB <- process(bc, verbose=verbose)
>> >> >> >
>> >> >> > 20100923 13:24:12|Background correcting data set...
>> >> >> >
>> >> >> > 20100923 13:24:12| Computing probe affinities...
>> >> >> >
>> >> >> > 20100923 13:24:12|  Computing GCRMA probe affinities for 1257006
>> >> >> > units...
>> >> >> >
>> >> >> > 20100923 13:24:12|   Identify PMs and MMs among the CDF cell
>> >> >> > indices...
>> >> >> >
>> >> >> >      logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >> >> >
>> >> >> >        Mode   FALSE    TRUE    NA's
>> >> >> >
>> >> >> >     logical  334476 4931683       0
>> >> >> >
>> >> >> > 20100923 13:25:57|    MMs are defined as non-PMs
>> >> >> >
>> >> >> > 20100923 13:25:57|    Number of PMs: 4931683
>> >> >> >
>> >> >> > 20100923 13:25:57|    Number of MMs: 334476
>> >> >> >
>> >> >> > 20100923 13:25:57|   Identify PMs and MMs among the CDF cell
>> >> >> > indices...done
>> >> >> >
>> >> >> > 20100923 13:25:57|   Reading probe-sequence data...
>> >> >> >
>> >> >> > 20100923 13:25:57|    Retrieving probe-sequence data...
>> >> >> >
>> >> >> > 20100923 13:25:57|     Chip type (full): MoEx-1_0-st-v1
>> >> >> >
>> >> >> > 20100923 13:25:57|     Locating probe-tab file...
>> >> >> >
>> >> >> > 20100923 13:25:57|      Chip type: MoEx-1_0-st-v1
>> >> >> >
>> >> >> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> >> >> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
>> >> >> > <environment>,
>> >> >> >  :
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > [2010-09-23 13:25:57] Exception: Found probe-tab file only by
>> >> >> > means
>> >> >> > of
>> >> >> > deprectated (v1) search rules:
>> >> >> >
>> >> >> >   at throw(Exception(...))
>> >> >> >
>> >> >> >   at throw.default("Found probe-tab file only by means of
>> >> >> > deprectated
>> >> >> > (v1
>> >> >> >
>> >> >> >   at throw("Found probe-tab file only by means of deprectated (v1)
>> >> >> > search
>> >> >> >
>> >> >> >   at method(static, ...)
>> >> >> >
>> >> >> >   at AffymetrixProbeTabFile$findByChipType(chipType, what = what,
>> >> >> > ...)
>> >> >> >
>> >> >> >   at method(static, ...)
>> >> >> >
>> >> >> >   at AffymetrixProbeTabFile$byChipType(chipType = chipType,
>> >> >> > verbose =
>> >> >> > les
>> >> >> >
>> >> >> >   at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe,
>> >> >> > verbose =
>> >> >> >
>> >> >> >   at getProbeSequenceData(this, safe = safe, verbose = verbose)
>> >> >> >
>> >> >> >   at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath,
>> >> >> > ...,
>> >> >> > ver
>> >> >> >
>> >> >> >   at computeAffinities(cdf, paths = probePath, ..., verbose =
>> >> >> > less(verbos
>> >> >> >
>> >> >> >   at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
>> >> >> > Data,GRBC/
>> >> >> >
>> >> >> >   at bgAdjustGcrma(NA, path = "probeData/Exon
>> >> >> > Data,GRBC/MoEx-1_0-st-v1",
>> >> >> >
>> >> >> >   at do.call("bgAdjustGcrma", args = args)
>> >> >> >
>> >> >> >   at process.GcRmaBackgroundCorrection(
>> >> >> >
>> >> >> > 20100923 13:25:57|     Locating probe-tab file...done
>> >> >> >
>> >> >> > 20100923 13:25:57|    Retrieving probe-sequence data...done
>> >> >> >
>> >> >> > 20100923 13:25:57|   Reading probe-sequence data...done
>> >> >> >
>> >> >> > 20100923 13:25:57|  Computing GCRMA probe affinities for 1257006
>> >> >> > units...done
>> >> >> >
>> >> >> > 20100923 13:25:57| Computing probe affinities...done
>> >> >> >
>> >> >> > 20100923 13:25:57|Background correcting data set...done
>> >> >> >
>> >> >> > Could anyone please enlighten me with the type of the error? I
>> >> >> > will
>> >> >> > be
>> >> >> > highly obliged if anyone please help me with this problem.
>> >> >> >
>> >> >> > Thank you.
>> >> >> >
>> >> >> > Prithish Banerjee.
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > When reporting problems on aroma.affymetrix, make sure 1) to run
>> >> >> > the
>> >> >> > latest
>> >> >> > version of the package, 2) to report the output of sessionInfo()
>> >> >> > and
>> >> >> > traceback(), and 3) to post a complete code example.
>> >> >> >
>> >> >> >
>> >> >> > You received this message because you are subscribed to the Google
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>> >> >> > http://www.aroma-project.org/.
>> >> >> > To post to this group, send email to
>> >> >> > [hidden email]
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>> >> >> >
>> >> >>
>> >> >> --
>> >> >> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> >> latest version of the package, 2) to report the output of
>> >> >> sessionInfo()
>> >> >> and
>> >> >> traceback(), and 3) to post a complete code example.
>> >> >>
>> >> >>
>> >> >> You received this message because you are subscribed to the Google
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>> >> >
>> >> > --
>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> > latest
>> >> > version of the package, 2) to report the output of sessionInfo() and
>> >> > traceback(), and 3) to post a complete code example.
>> >> >
>> >> >
>> >> > You received this message because you are subscribed to the Google
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>> >>
>> >> --
>> >> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> latest version of the package, 2) to report the output of sessionInfo()
>> >> and
>> >> traceback(), and 3) to post a complete code example.
>> >>
>> >>
>> >> You received this message because you are subscribed to the Google
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>> >
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
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>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
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>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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