[aroma.affymetrix] Help Regarding GCRMA Human Exon.

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[aroma.affymetrix] Help Regarding GCRMA Human Exon.

Prithish Banerjee
Respected Dr Bengtsson,

I have the following codes and outputs:

> hbInstall("aroma.affymetrix")
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE); 
> dataSet <- "Exon Data"
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
Filesize: 203.31MB
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 297051
Cells per unit: 22.06
Number of QC units: 1
> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
> print(ptf)
AffymetrixProbeTabFile:
Name: HuEx-1_0-st-v2
Tags: 
Full name: HuEx-1_0-st-v2
Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
File size: 527.80 MB (553438704 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
Filesize: 38.25MB
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18708
Cells per unit: 350.31
Number of QC units: 1
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags: 
Path: rawData/Exon Data/HuEx-1_0-st-v2
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Number of arrays: 17
Names: 10_5N, 11_6T, ..., 9_5T
Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
Total file size: 1081.22MB
RAM: 0.02MB
> 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: 17 (1081.22MB)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
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/HuEx-1_0-st-v2
Is done: FALSE
RAM: 0.00MB
> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
20101202 14:46:02|Background correcting data set...
20101202 14:46:02| Computing probe affinities (independent of data)...
20101202 14:46:03|  Computing GCRMA probe affinities...
20101202 14:46:03|   Chip type: HuEx-1_0-st-v2
20101202 14:46:03|   Number of units: 297051
20101202 14:46:03|   Locating the cell sequence annotation data file...
20101202 14:46:03|   Locating the cell sequence annotation data file...done
20101202 14:46:03|  Computing GCRMA probe affinities...done
20101202 14:46:03|  Computing GCRMA probe affinities...
20101202 14:46:03|   Number of units: 297051
20101202 14:46:03|   Identify PMs and MMs among the CDF cell indices...
     logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
       Mode    TRUE    NA's 
    logical 5270074       0 
20101202 14:46:52|    MMs are defined as non-PMs
20101202 14:46:52|    Number of PMs: 5270074
20101202 14:46:52|    Number of MMs: 0
20101202 14:46:52|   Identify PMs and MMs among the CDF cell indices...done
20101202 14:46:52|   Reading probe-sequence data...
20101202 14:46:52|    Retrieving probe-sequence data...
20101202 14:46:52|     Chip type (full): HuEx-1_0-st-v2,fullR3,A20071112,EP
20101202 14:46:52|     Locating probe-tab file...
20101202 14:46:52|      Chip type: HuEx-1_0-st-v2
      AffymetrixProbeTabFile:
      Name: HuEx-1_0-st-v2
      Tags: 
      Full name: HuEx-1_0-st-v2
      Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
      File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
      Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
      Filesize: 38.25MB
      Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
      RAM: 0.00MB
      File format: v4 (binary; XDA)
      Dimension: 2560x2560
      Number of cells: 6553600
      Number of units: 18708
      Cells per unit: 350.31
      Number of QC units: 1
20101202 14:46:52|     Locating probe-tab file...done
20101202 14:46:52|     Validating probe-tab file against CDF...
20101202 14:46:52|      Number of records read: 1
20101202 14:46:52|      Data read:
      'data.frame': 1 obs. of  1 variable:
       $ probeSetID: chr "2315101"
       - attr(*, "fileHeader")=List of 6
        ..$ comments: NULL
        ..$ sep     : chr "\t"
        ..$ quote   : chr "\""
        ..$ skip    : num 0
        ..$ topRows :List of 10
        .. ..$ : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
        .. ..$ : chr  "494998" "2315101" "917" "193" ...
        .. ..$ : chr  "1734213" "2315101" "1092" "677" ...
        .. ..$ : chr  "4767517" "2315101" "796" "1862" ...
        .. ..$ : chr  "4286427" "2315101" "986" "1674" ...
        .. ..$ : chr  "5760145" "2315102" "144" "2250" ...
        .. ..$ : chr  "671410" "2315102" "689" "262" ...
        .. ..$ : chr  "4275780" "2315102" "579" "1670" ...
        .. ..$ : chr  "4293462" "2315102" "341" "1677" ...
        .. ..$ : chr  "5388" "2315103" "267" "2" ...
        ..$ columns : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
20101202 14:46:52|      Unit name:
       chr "2315101"
20101202 14:46:55|      Unit index: NA
Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` = <environment>,  : 
  
[2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit name '2315101': annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
  at throw(Exception(...))
  at throw.default("Failed to identify CDF unit with unit name '", unitNa
  at throw("Failed to identify CDF unit with unit name '", unitName, "': 
  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/HuEx-1_0-st-v2", 
  at do.call("bgAdjustGcrma", args = args)
  at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose 
  at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
20101202 14:46:55|     Validating probe-tab file against CDF...done
20101202 14:46:55|    Retrieving probe-sequence data...done
20101202 14:46:55|   Reading probe-sequence data...done
20101202 14:46:55|  Computing GCRMA probe affinities...done
20101202 14:46:55| Computing probe affinities (independent of data)...done
20101202 14:46:55|Background correcting data set...done


Could you please tell me how to rectify the error?

Thank you.

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

--
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 Regarding GCRMA Human Exon.

Henrik Bengtsson-4
Hi.

On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee
<[hidden email]> wrote:
> Respected Dr Bengtsson,
> I have the following codes and outputs:
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")

I'll assume that you've run this recently so that you have
aroma.affymetrix v1.8.0 installed, because then you can do what I
explain next.  FYI, whenever you get an error, please report what
sessionInfo() gives so we can be sure you're up-to-date.

Go to the HuEx-1_0-st-v2 chip type page:

   http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/

and download the Aroma Cell Sequence (ACS) file.  Place it in
annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is).  Don't
forget to gunzip.

You can drop/move/leave the probe-tab file; it won't be needed anymore.

The following script should do:

verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Exon Data";
chipType <- "HuEx-1_0-st-v2";
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
print(cdf);

# Assert that the ACS file is available (not really needed to be done)
acs <- getAromaCellSequenceFile(cdf);
print(acs);

# GCRMA background correction
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
print(csB);

Finally, I've noticed that you've tried to pass arguments 'cdf' and
'ptf' to process(), i.e.

csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose);

That is not correct.  Was that suggested to you anywhere, or is it
just part of your trial-and-error?

Let me know if this solves your problem

/Henrik

>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data"
>> chipType <- "HuEx-1_0-st-v2"
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
> Filesize: 203.31MB
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 297051
> Cells per unit: 22.06
> Number of QC units: 1
>> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
>> print(ptf)
> AffymetrixProbeTabFile:
> Name: HuEx-1_0-st-v2
> Tags:
> Full name: HuEx-1_0-st-v2
> Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
> File size: 527.80 MB (553438704 bytes)
> RAM: 0.01 MB
> Number of data rows: NA
> Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly',
> 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness',
> 'category'
> Number of text lines: NA
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
> Filesize: 38.25MB
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 18708
> Cells per unit: 350.31
> Number of QC units: 1
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
>> print(csR)
> AffymetrixCelSet:
> Name: Exon Data
> Tags:
> Path: rawData/Exon Data/HuEx-1_0-st-v2
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> Number of arrays: 17
> Names: 10_5N, 11_6T, ..., 9_5T
> Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
> Total file size: 1081.22MB
> RAM: 0.02MB
>> 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: 17 (1081.22MB)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> 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/HuEx-1_0-st-v2
> Is done: FALSE
> RAM: 0.00MB
>> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
> 20101202 14:46:02|Background correcting data set...
> 20101202 14:46:02| Computing probe affinities (independent of data)...
> 20101202 14:46:03|  Computing GCRMA probe affinities...
> 20101202 14:46:03|   Chip type: HuEx-1_0-st-v2
> 20101202 14:46:03|   Number of units: 297051
> 20101202 14:46:03|   Locating the cell sequence annotation data file...
> 20101202 14:46:03|   Locating the cell sequence annotation data file...done
> 20101202 14:46:03|  Computing GCRMA probe affinities...done
> 20101202 14:46:03|  Computing GCRMA probe affinities...
> 20101202 14:46:03|   Number of units: 297051
> 20101202 14:46:03|   Identify PMs and MMs among the CDF cell indices...
>      logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
>        Mode    TRUE    NA's
>     logical 5270074       0
> 20101202 14:46:52|    MMs are defined as non-PMs
> 20101202 14:46:52|    Number of PMs: 5270074
> 20101202 14:46:52|    Number of MMs: 0
> 20101202 14:46:52|   Identify PMs and MMs among the CDF cell indices...done
> 20101202 14:46:52|   Reading probe-sequence data...
> 20101202 14:46:52|    Retrieving probe-sequence data...
> 20101202 14:46:52|     Chip type (full): HuEx-1_0-st-v2,fullR3,A20071112,EP
> 20101202 14:46:52|     Locating probe-tab file...
> 20101202 14:46:52|      Chip type: HuEx-1_0-st-v2
>       AffymetrixProbeTabFile:
>       Name: HuEx-1_0-st-v2
>       Tags:
>       Full name: HuEx-1_0-st-v2
>       Pathname:
> annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>       File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
>       Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>       Filesize: 38.25MB
>       Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>       RAM: 0.00MB
>       File format: v4 (binary; XDA)
>       Dimension: 2560x2560
>       Number of cells: 6553600
>       Number of units: 18708
>       Cells per unit: 350.31
>       Number of QC units: 1
> 20101202 14:46:52|     Locating probe-tab file...done
> 20101202 14:46:52|     Validating probe-tab file against CDF...
> 20101202 14:46:52|      Number of records read: 1
> 20101202 14:46:52|      Data read:
>       'data.frame': 1 obs. of  1 variable:
>        $ probeSetID: chr "2315101"
>        - attr(*, "fileHeader")=List of 6
>         ..$ comments: NULL
>         ..$ sep     : chr "\t"
>         ..$ quote   : chr "\""
>         ..$ skip    : num 0
>         ..$ topRows :List of 10
>         .. ..$ : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
>         .. ..$ : chr  "494998" "2315101" "917" "193" ...
>         .. ..$ : chr  "1734213" "2315101" "1092" "677" ...
>         .. ..$ : chr  "4767517" "2315101" "796" "1862" ...
>         .. ..$ : chr  "4286427" "2315101" "986" "1674" ...
>         .. ..$ : chr  "5760145" "2315102" "144" "2250" ...
>         .. ..$ : chr  "671410" "2315102" "689" "262" ...
>         .. ..$ : chr  "4275780" "2315102" "579" "1670" ...
>         .. ..$ : chr  "4293462" "2315102" "341" "1677" ...
>         .. ..$ : chr  "5388" "2315103" "267" "2" ...
>         ..$ columns : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
> 20101202 14:46:52|      Unit name:
>        chr "2315101"
> 20101202 14:46:55|      Unit index: NA
> Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` =
> <environment>,  :
>
> [2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit name
> '2315101': annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>   at throw(Exception(...))
>   at throw.default("Failed to identify CDF unit with unit name '", unitNa
>   at throw("Failed to identify CDF unit with unit name '", unitName, "':
>   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/HuEx-1_0-st-v2",
>   at do.call("bgAdjustGcrma", args = args)
>   at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
>   at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
> 20101202 14:46:55|     Validating probe-tab file against CDF...done
> 20101202 14:46:55|    Retrieving probe-sequence data...done
> 20101202 14:46:55|   Reading probe-sequence data...done
> 20101202 14:46:55|  Computing GCRMA probe affinities...done
> 20101202 14:46:55| Computing probe affinities (independent of data)...done
> 20101202 14:46:55|Background correcting data set...done
>
> Could you please tell me how to rectify the error?
> Thank you.
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> --
> 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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[aroma.affymetrix]

Yan Jiao
Hi,

First of all, I have to say I've got tremendous help from this mailing list, thank you for all of you.
Then I have to continue asking for help,
I just realize I probably did something very stupid,
I was doing DNA copy number segmentation, affymetrix 100k SNP, so as far as I know there are two chips, one chip is obtained by digesting the DNA with Hind, the other chip by Xba.Chip, so in my rawdata folder , I got the .CEL file from both, but in the annotationData folder, sub folder :type, I only got  Mapping50K_Hind240,and .cdf file, .ufl, ugp file for hind.
My question is, Should I firstly split the .cel file accoding to the chip type and then found the corresponding cdf file etc for Xba.

Many thanks

Yan

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 03 December 2010 07:50
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] Help Regarding GCRMA Human Exon.

Hi.

On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee
<[hidden email]> wrote:
> Respected Dr Bengtsson,
> I have the following codes and outputs:
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")

I'll assume that you've run this recently so that you have
aroma.affymetrix v1.8.0 installed, because then you can do what I
explain next.  FYI, whenever you get an error, please report what
sessionInfo() gives so we can be sure you're up-to-date.

Go to the HuEx-1_0-st-v2 chip type page:

   http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/

and download the Aroma Cell Sequence (ACS) file.  Place it in
annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is).  Don't
forget to gunzip.

You can drop/move/leave the probe-tab file; it won't be needed anymore.

The following script should do:

verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Exon Data";
chipType <- "HuEx-1_0-st-v2";
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
print(cdf);

# Assert that the ACS file is available (not really needed to be done)
acs <- getAromaCellSequenceFile(cdf);
print(acs);

# GCRMA background correction
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
print(csB);

Finally, I've noticed that you've tried to pass arguments 'cdf' and
'ptf' to process(), i.e.

csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose);

That is not correct.  Was that suggested to you anywhere, or is it
just part of your trial-and-error?

Let me know if this solves your problem

/Henrik

>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data"
>> chipType <- "HuEx-1_0-st-v2"
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
> Filesize: 203.31MB
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 297051
> Cells per unit: 22.06
> Number of QC units: 1
>> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
>> print(ptf)
> AffymetrixProbeTabFile:
> Name: HuEx-1_0-st-v2
> Tags:
> Full name: HuEx-1_0-st-v2
> Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
> File size: 527.80 MB (553438704 bytes)
> RAM: 0.01 MB
> Number of data rows: NA
> Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly',
> 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness',
> 'category'
> Number of text lines: NA
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
> Filesize: 38.25MB
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 18708
> Cells per unit: 350.31
> Number of QC units: 1
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
>> print(csR)
> AffymetrixCelSet:
> Name: Exon Data
> Tags:
> Path: rawData/Exon Data/HuEx-1_0-st-v2
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> Number of arrays: 17
> Names: 10_5N, 11_6T, ..., 9_5T
> Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
> Total file size: 1081.22MB
> RAM: 0.02MB
>> 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: 17 (1081.22MB)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> 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/HuEx-1_0-st-v2
> Is done: FALSE
> RAM: 0.00MB
>> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
> 20101202 14:46:02|Background correcting data set...
> 20101202 14:46:02| Computing probe affinities (independent of data)...
> 20101202 14:46:03|  Computing GCRMA probe affinities...
> 20101202 14:46:03|   Chip type: HuEx-1_0-st-v2
> 20101202 14:46:03|   Number of units: 297051
> 20101202 14:46:03|   Locating the cell sequence annotation data file...
> 20101202 14:46:03|   Locating the cell sequence annotation data file...done
> 20101202 14:46:03|  Computing GCRMA probe affinities...done
> 20101202 14:46:03|  Computing GCRMA probe affinities...
> 20101202 14:46:03|   Number of units: 297051
> 20101202 14:46:03|   Identify PMs and MMs among the CDF cell indices...
>      logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
>        Mode    TRUE    NA's
>     logical 5270074       0
> 20101202 14:46:52|    MMs are defined as non-PMs
> 20101202 14:46:52|    Number of PMs: 5270074
> 20101202 14:46:52|    Number of MMs: 0
> 20101202 14:46:52|   Identify PMs and MMs among the CDF cell indices...done
> 20101202 14:46:52|   Reading probe-sequence data...
> 20101202 14:46:52|    Retrieving probe-sequence data...
> 20101202 14:46:52|     Chip type (full): HuEx-1_0-st-v2,fullR3,A20071112,EP
> 20101202 14:46:52|     Locating probe-tab file...
> 20101202 14:46:52|      Chip type: HuEx-1_0-st-v2
>       AffymetrixProbeTabFile:
>       Name: HuEx-1_0-st-v2
>       Tags:
>       Full name: HuEx-1_0-st-v2
>       Pathname:
> annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>       File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
>       Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>       Filesize: 38.25MB
>       Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>       RAM: 0.00MB
>       File format: v4 (binary; XDA)
>       Dimension: 2560x2560
>       Number of cells: 6553600
>       Number of units: 18708
>       Cells per unit: 350.31
>       Number of QC units: 1
> 20101202 14:46:52|     Locating probe-tab file...done
> 20101202 14:46:52|     Validating probe-tab file against CDF...
> 20101202 14:46:52|      Number of records read: 1
> 20101202 14:46:52|      Data read:
>       'data.frame': 1 obs. of  1 variable:
>        $ probeSetID: chr "2315101"
>        - attr(*, "fileHeader")=List of 6
>         ..$ comments: NULL
>         ..$ sep     : chr "\t"
>         ..$ quote   : chr "\""
>         ..$ skip    : num 0
>         ..$ topRows :List of 10
>         .. ..$ : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
>         .. ..$ : chr  "494998" "2315101" "917" "193" ...
>         .. ..$ : chr  "1734213" "2315101" "1092" "677" ...
>         .. ..$ : chr  "4767517" "2315101" "796" "1862" ...
>         .. ..$ : chr  "4286427" "2315101" "986" "1674" ...
>         .. ..$ : chr  "5760145" "2315102" "144" "2250" ...
>         .. ..$ : chr  "671410" "2315102" "689" "262" ...
>         .. ..$ : chr  "4275780" "2315102" "579" "1670" ...
>         .. ..$ : chr  "4293462" "2315102" "341" "1677" ...
>         .. ..$ : chr  "5388" "2315103" "267" "2" ...
>         ..$ columns : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
> 20101202 14:46:52|      Unit name:
>        chr "2315101"
> 20101202 14:46:55|      Unit index: NA
> Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` =
> <environment>,  :
>
> [2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit name
> '2315101': annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>   at throw(Exception(...))
>   at throw.default("Failed to identify CDF unit with unit name '", unitNa
>   at throw("Failed to identify CDF unit with unit name '", unitName, "':
>   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/HuEx-1_0-st-v2",
>   at do.call("bgAdjustGcrma", args = args)
>   at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
>   at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
> 20101202 14:46:55|     Validating probe-tab file against CDF...done
> 20101202 14:46:55|    Retrieving probe-sequence data...done
> 20101202 14:46:55|   Reading probe-sequence data...done
> 20101202 14:46:55|  Computing GCRMA probe affinities...done
> 20101202 14:46:55| Computing probe affinities (independent of data)...done
> 20101202 14:46:55|Background correcting data set...done
>
> Could you please tell me how to rectify the error?
> Thank you.
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> --
> 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 Regarding GCRMA Human Exon.

Prithish Banerjee
In reply to this post by Henrik Bengtsson-4
Respected Dr Bengtsson,

Thank you for your help. Sorry for not providing the sessionInfo() last time. I am using aroma.affymetrix v 1.8.0. It solved that error but I am facing a new error this time. The sessionInfo and the outputs are as follows:

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

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_1.8.0 aroma.apd_0.1.7        affxparser_1.22.0     
 [4] R.huge_0.2.0           aroma.core_1.8.0       aroma.light_1.18.2    
 [7] matrixStats_0.2.2      R.rsp_0.4.0            R.filesets_0.9.1      
[10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.8         
[13] R.oo_1.7.4             R.methodsS3_1.2.1     

loaded via a namespace (and not attached):
[1] affy_1.28.0           affyio_1.18.0         Biobase_2.10.0       
[4] Biostrings_2.18.0     gcrma_2.22.0          IRanges_1.8.2        
[7] preprocessCore_1.12.0 splines_2.12.0        tools_2.12.0    


> hbInstall("aroma.affymetrix")
> hbInstall("aroma.cn")
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE); 
> dataSet <- "Exon Data"
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
> print(cdf)
> acs<-getAromaCellSequenceFile(cdf)
> print(acs)
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
> 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: 4 (251.42MB)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
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/HuEx-1_0-st-v2
Is done: FALSE
RAM: 0.00MB
> csB <- process(bc, verbose=verbose)
20101203 14:04:42|Background correcting data set...
20101203 14:04:42| Computing probe affinities (independent of data)...
20101203 14:04:42|  Computing GCRMA probe affinities...
20101203 14:04:42|   Chip type: HuEx-1_0-st-v2
20101203 14:04:42|   Number of units: 297051
20101203 14:04:43|   Cached results found.
20101203 14:04:43|  Computing GCRMA probe affinities...done
20101203 14:04:43|  RAM: 50.00MB
20101203 14:04:43| Computing probe affinities (independent of data)...done
20101203 14:04:43| Background correcting data set...
20101203 14:04:44|  Already background corrected for "optical" effects
20101203 14:04:44| Background correcting data set...done
20101203 14:04:44| Estimating specific binding parameters (data dependent)...
20101203 14:04:44|  Extracting PM indices...
20101203 14:04:44|   Reading cell indices from CDF file...
20101203 14:04:44|    Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
20101203 14:04:44|    Units: 
     NULL
20101203 14:04:44|    lapplyInChunks()...
20101203 14:04:44|     Number of elements per chunk: 1e+05
20101203 14:04:44|     Chunk #1 of 3...
20101203 14:04:44|      Elements: 
       int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
20101203 14:04:44|      Querying CDF file...
20101203 14:05:08|      Querying CDF file...done
20101203 14:05:08|      Restructuring...
20101203 14:05:08|      Restructuring...done
                 used  (Mb) gc trigger  (Mb) max used  (Mb)
      Ncells  5354837 143.0    6193578 165.4  5373715 143.5
      Vcells 13471411 102.8   20149605 153.8 13475095 102.9
20101203 14:05:09|     Chunk #1 of 3...done
20101203 14:05:09|     Chunk #2 of 3...
20101203 14:05:09|      Elements: 
       int [1:100000] 100001 100002 100003 100004 100005 100006 100007 100008 100009 100010 ...
20101203 14:05:09|      Querying CDF file...
20101203 14:05:15|      Querying CDF file...done
20101203 14:05:15|      Restructuring...
20101203 14:05:15|      Restructuring...done
                 used (Mb) gc trigger  (Mb) max used  (Mb)
      Ncells  1491395 39.9    4954862 132.4  6193578 165.4
      Vcells 10685280 81.6   20149605 153.8 17357812 132.5
20101203 14:05:16|     Chunk #2 of 3...done
20101203 14:05:16|     Chunk #3 of 3...
20101203 14:05:16|      Elements: 
       int [1:97051] 200001 200002 200003 200004 200005 200006 200007 200008 200009 200010 ...
20101203 14:05:16|      Querying CDF file...
20101203 14:05:20|      Querying CDF file...done
20101203 14:05:21|      Restructuring...
20101203 14:05:21|      Restructuring...done
                 used (Mb) gc trigger  (Mb) max used  (Mb)
      Ncells  1471326 39.3    4954862 132.4  6193578 165.4
      Vcells 10882001 83.1   20149605 153.8 17357812 132.5
20101203 14:05:21|     Chunk #3 of 3...done
20101203 14:05:21|    lapplyInChunks()...done
20101203 14:05:21|   Reading cell indices from CDF file...done
             used (Mb) gc trigger  (Mb) max used  (Mb)
   Ncells  336599  9.0    3963889 105.9  6193578 165.4
   Vcells 9592574 73.2   20149605 153.8 17357812 132.5
20101203 14:05:21|   readUnits.AffymetrixCdfFile(): Updating cache
20101203 14:05:49|  Extracting PM indices...done
            used (Mb) gc trigger  (Mb) max used  (Mb)
  Ncells  336674  9.0    2849399  76.1  6193578 165.4
  Vcells 7232054 55.2   23577885 179.9 23043337 175.9
20101203 14:05:49|  Extracting 25000 random PM intensities across CEL set...
20101203 14:05:49|   Array #1 of 4...
20101203 14:05:50|   Array #1 of 4...done
20101203 14:05:50|   Array #2 of 4...
20101203 14:05:50|   Array #2 of 4...done
20101203 14:05:50|   Array #3 of 4...
20101203 14:05:50|   Array #3 of 4...done
20101203 14:05:50|   Array #4 of 4...
20101203 14:05:50|   Array #4 of 4...done
             used (Mb) gc trigger  (Mb) max used  (Mb)
   Ncells  337074  9.1    2279519  60.9  6193578 165.4
   Vcells 7257179 55.4   23577885 179.9 23043337 175.9
20101203 14:05:50|  Extracting 25000 random PM intensities across CEL set...done
20101203 14:05:50|  Extracting probe affinities and fitting linear model...
             used (Mb) gc trigger  (Mb) max used  (Mb)
   Ncells  337074  9.1    1823615  48.7  6193578 165.4
   Vcells 7269671 55.5   23577885 179.9 23043337 175.9
20101203 14:05:51|   Fitting the GCRMA background linear model...
     num [1:25000] 6.13 10.17 5.73 7.87 10.87 ...
     num [1:25000] 0.097 0.771 0.181 0.443 1.88 ...
    
    Call:
    lm(formula = pm.random2 ~ aff)
    
    Coefficients:
    (Intercept)          aff  
          7.104        0.597  
    
20101203 14:05:51|   Fitting the GCRMA background linear model...done
20101203 14:05:51|  Extracting probe affinities and fitting linear model...done
20101203 14:05:51|  parametersGsb:
  (Intercept)         aff 
    7.1042892   0.5969684 
20101203 14:05:51| Estimating specific binding parameters (data dependent)...done
20101203 14:05:51| Adjusting 4 arrays...
20101203 14:05:51|  Array #1 of 4...
   AffymetrixCelFile:
   Name: 10 ZEB1_(HuEx-1_0-st-v2)
   Tags: 
   Full name: 10 ZEB1_(HuEx-1_0-st-v2)
   Pathname: probeData/Exon Data,OBC/HuEx-1_0-st-v2/10 ZEB1_(HuEx-1_0-st-v2).CEL
   File size: 62.50 MB (65536714 bytes)
   RAM: 0.00 MB
   File format: v4 (binary; XDA)
   Platform: Affymetrix
   Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
   Timestamp: 2010-12-03 13:43:43
20101203 14:05:51|   Retrieving PM and MM signals and affinities...
20101203 14:06:26|    Number of PM probes: 5270074
20101203 14:06:26|    Number of MM probes: 0
20101203 14:06:42|    PM signals:
     num [1:5270074] 237 480 120 482 421 ...
20101203 14:06:42|    MM signals:
     num(0) 
20101203 14:06:43|    PM affinities:
     num [1:5270074] -0.585 -1.687 -1.664 -0.569 1.626 ...
20101203 14:06:43|    MM affinities:
     num(0) 
20101203 14:06:43|   Retrieving PM and MM signals and affinities...done
20101203 14:06:43|   Estimating non-specific binding parameters...
20101203 14:06:43|    Model type/flavor: affinities
20101203 14:06:43|    Affinity-based GCRMA model background adjustment...
20101203 14:06:43|     Using mismatch probes (MMs) as negative controls
20101203 14:06:43|     Dropping perfect-match probes (PMs) with missing signals or missing affinities...
20101203 14:06:43|      Number of finite PMs: 5270074 out of 5270074 (100.0%)
20101203 14:06:43|      Number of finite PM affinities: 5270074 out of 5270074 (100.0%)
20101203 14:06:44|      Number of PMs kept: 5270074 out of 5270074 (100.0%)
20101203 14:06:45|     Dropping perfect-match probes (PMs) with missing signals or missing affinities...done
20101203 14:06:45|     Dropping negative controls with missing signals or missing affinities...
20101203 14:06:45|      Number of finite negative controls: 0 out of 0 (NaN%)
20101203 14:06:45|      Number of finite negative-control affinities: 0 out of 0 (NaN%)
20101203 14:06:45|      Number of negative controls kept: 0 out of 0 (NaN%)
20101203 14:06:45|     Dropping negative controls with missing signals or missing affinities...done
20101203 14:06:45|     Number of PMs: 5270074
20101203 14:06:45|     Number of negative controls: 0
Error in if (from == to) rep.int(from, length.out) else as.vector(c(from,  : 
  missing value where TRUE/FALSE needed
20101203 14:06:49|  Array #1 of 4...done
20101203 14:06:49| Adjusting 4 arrays...done
20101203 14:06:49|Background correcting data set...done


Please help me in this regard. Also The passing of cdf and ptf arguments in process() is just the trial-error I was trying. I am really sorry for that and should have given you the code I have.

Yours Faithfully,

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

On Fri, Dec 3, 2010 at 2:50 AM, Henrik Bengtsson <[hidden email]> wrote:
Hi.

On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee
<[hidden email]> wrote:
> Respected Dr Bengtsson,
> I have the following codes and outputs:
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")

I'll assume that you've run this recently so that you have
aroma.affymetrix v1.8.0 installed, because then you can do what I
explain next.  FYI, whenever you get an error, please report what
sessionInfo() gives so we can be sure you're up-to-date.

Go to the HuEx-1_0-st-v2 chip type page:

  http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/

and download the Aroma Cell Sequence (ACS) file.  Place it in
annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is).  Don't
forget to gunzip.

You can drop/move/leave the probe-tab file; it won't be needed anymore.

The following script should do:

verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Exon Data";
chipType <- "HuEx-1_0-st-v2";
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
print(cdf);

# Assert that the ACS file is available (not really needed to be done)
acs <- getAromaCellSequenceFile(cdf);
print(acs);

# GCRMA background correction
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
print(csB);

Finally, I've noticed that you've tried to pass arguments 'cdf' and
'ptf' to process(), i.e.

csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose);

That is not correct.  Was that suggested to you anywhere, or is it
just part of your trial-and-error?

Let me know if this solves your problem

/Henrik

>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data"
>> chipType <- "HuEx-1_0-st-v2"
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
> Filesize: 203.31MB
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 297051
> Cells per unit: 22.06
> Number of QC units: 1
>> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
>> print(ptf)
> AffymetrixProbeTabFile:
> Name: HuEx-1_0-st-v2
> Tags:
> Full name: HuEx-1_0-st-v2
> Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
> File size: 527.80 MB (553438704 bytes)
> RAM: 0.01 MB
> Number of data rows: NA
> Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly',
> 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness',
> 'category'
> Number of text lines: NA
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
> Filesize: 38.25MB
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 18708
> Cells per unit: 350.31
> Number of QC units: 1
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
>> print(csR)
> AffymetrixCelSet:
> Name: Exon Data
> Tags:
> Path: rawData/Exon Data/HuEx-1_0-st-v2
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> Number of arrays: 17
> Names: 10_5N, 11_6T, ..., 9_5T
> Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
> Total file size: 1081.22MB
> RAM: 0.02MB
>> 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: 17 (1081.22MB)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> 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/HuEx-1_0-st-v2
> Is done: FALSE
> RAM: 0.00MB
>> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
> 20101202 14:46:02|Background correcting data set...
> 20101202 14:46:02| Computing probe affinities (independent of data)...
> 20101202 14:46:03|  Computing GCRMA probe affinities...
> 20101202 14:46:03|   Chip type: HuEx-1_0-st-v2
> 20101202 14:46:03|   Number of units: 297051
> 20101202 14:46:03|   Locating the cell sequence annotation data file...
> 20101202 14:46:03|   Locating the cell sequence annotation data file...done
> 20101202 14:46:03|  Computing GCRMA probe affinities...done
> 20101202 14:46:03|  Computing GCRMA probe affinities...
> 20101202 14:46:03|   Number of units: 297051
> 20101202 14:46:03|   Identify PMs and MMs among the CDF cell indices...
>      logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
>        Mode    TRUE    NA's
>     logical 5270074       0
> 20101202 14:46:52|    MMs are defined as non-PMs
> 20101202 14:46:52|    Number of PMs: 5270074
> 20101202 14:46:52|    Number of MMs: 0
> 20101202 14:46:52|   Identify PMs and MMs among the CDF cell indices...done
> 20101202 14:46:52|   Reading probe-sequence data...
> 20101202 14:46:52|    Retrieving probe-sequence data...
> 20101202 14:46:52|     Chip type (full): HuEx-1_0-st-v2,fullR3,A20071112,EP
> 20101202 14:46:52|     Locating probe-tab file...
> 20101202 14:46:52|      Chip type: HuEx-1_0-st-v2
>       AffymetrixProbeTabFile:
>       Name: HuEx-1_0-st-v2
>       Tags:
>       Full name: HuEx-1_0-st-v2
>       Pathname:
> annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>       File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
>       Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>       Filesize: 38.25MB
>       Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>       RAM: 0.00MB
>       File format: v4 (binary; XDA)
>       Dimension: 2560x2560
>       Number of cells: 6553600
>       Number of units: 18708
>       Cells per unit: 350.31
>       Number of QC units: 1
> 20101202 14:46:52|     Locating probe-tab file...done
> 20101202 14:46:52|     Validating probe-tab file against CDF...
> 20101202 14:46:52|      Number of records read: 1
> 20101202 14:46:52|      Data read:
>       'data.frame': 1 obs. of  1 variable:
>        $ probeSetID: chr "2315101"
>        - attr(*, "fileHeader")=List of 6
>         ..$ comments: NULL
>         ..$ sep     : chr "\t"
>         ..$ quote   : chr "\""
>         ..$ skip    : num 0
>         ..$ topRows :List of 10
>         .. ..$ : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
>         .. ..$ : chr  "494998" "2315101" "917" "193" ...
>         .. ..$ : chr  "1734213" "2315101" "1092" "677" ...
>         .. ..$ : chr  "4767517" "2315101" "796" "1862" ...
>         .. ..$ : chr  "4286427" "2315101" "986" "1674" ...
>         .. ..$ : chr  "5760145" "2315102" "144" "2250" ...
>         .. ..$ : chr  "671410" "2315102" "689" "262" ...
>         .. ..$ : chr  "4275780" "2315102" "579" "1670" ...
>         .. ..$ : chr  "4293462" "2315102" "341" "1677" ...
>         .. ..$ : chr  "5388" "2315103" "267" "2" ...
>         ..$ columns : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
> 20101202 14:46:52|      Unit name:
>        chr "2315101"
> 20101202 14:46:55|      Unit index: NA
> Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` =
> <environment>,  :
>
> [2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit name
> '2315101': annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>   at throw(Exception(...))
>   at throw.default("Failed to identify CDF unit with unit name '", unitNa
>   at throw("Failed to identify CDF unit with unit name '", unitName, "':
>   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/HuEx-1_0-st-v2",
>   at do.call("bgAdjustGcrma", args = args)
>   at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
>   at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
> 20101202 14:46:55|     Validating probe-tab file against CDF...done
> 20101202 14:46:55|    Retrieving probe-sequence data...done
> 20101202 14:46:55|   Reading probe-sequence data...done
> 20101202 14:46:55|  Computing GCRMA probe affinities...done
> 20101202 14:46:55| Computing probe affinities (independent of data)...done
> 20101202 14:46:55|Background correcting data set...done
>
> Could you please tell me how to rectify the error?
> Thank you.
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
>
> --
> 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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>

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Re: [aroma.affymetrix] Help Regarding GCRMA Human Exon.

Henrik Bengtsson-4
Hi,

sorry, it turns out that you also have to use the unsupported CDF for
the GCRMA step.  It is only needed for that step, hence the setCdf():s
set & undo.  You can download a binary version of HuEx-1_0-st-v2.cdf
at:

  http://aroma-project.org/chipTypes/HuEx-1_0-st-v2

Then do:

library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);

dataSet <- "Exon Data";
chipType <- "HuEx-1_0-st-v2";

# The unsupported CDF
cdfS <- AffymetrixCdfFile$byChipType(chipType);
print(cdfS);

# The custom CDF
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
print(cdf);

# Setup data set
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);

# GCRMA background correction
setCdf(csR, cdfS); # Set temporarily
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
setCdf(csR, cdf); # Undo.
setCdf(csB, cdf); # Undo.
print(csB);

That should do it.

FYI, when doing AffymetrixCelSet$byName(...) specify either argument
'chipType' or 'cdf' - not both.

/Henrik

On Fri, Dec 3, 2010 at 11:22 AM, Prithish Banerjee
<[hidden email]> wrote:

> Respected Dr Bengtsson,
> Thank you for your help. Sorry for not providing the sessionInfo() last
> time. I am using aroma.affymetrix v 1.8.0. It solved that error but I am
> facing a new error this time. The sessionInfo and the outputs are as
> follows:
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 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_1.8.0 aroma.apd_0.1.7        affxparser_1.22.0
>  [4] R.huge_0.2.0           aroma.core_1.8.0       aroma.light_1.18.2
>  [7] matrixStats_0.2.2      R.rsp_0.4.0            R.filesets_0.9.1
> [10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.8
> [13] R.oo_1.7.4             R.methodsS3_1.2.1
> loaded via a namespace (and not attached):
> [1] affy_1.28.0           affyio_1.18.0         Biobase_2.10.0
> [4] Biostrings_2.18.0     gcrma_2.22.0          IRanges_1.8.2
> [7] preprocessCore_1.12.0 splines_2.12.0        tools_2.12.0
>
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.cn")
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data"
>> chipType <- "HuEx-1_0-st-v2"
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
>> print(cdf)
>> acs<-getAromaCellSequenceFile(cdf)
>> print(acs)
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
>> 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: 4 (251.42MB)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> 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/HuEx-1_0-st-v2
> Is done: FALSE
> RAM: 0.00MB
>> csB <- process(bc, verbose=verbose)
> 20101203 14:04:42|Background correcting data set...
> 20101203 14:04:42| Computing probe affinities (independent of data)...
> 20101203 14:04:42|  Computing GCRMA probe affinities...
> 20101203 14:04:42|   Chip type: HuEx-1_0-st-v2
> 20101203 14:04:42|   Number of units: 297051
> 20101203 14:04:43|   Cached results found.
> 20101203 14:04:43|  Computing GCRMA probe affinities...done
> 20101203 14:04:43|  RAM: 50.00MB
> 20101203 14:04:43| Computing probe affinities (independent of data)...done
> 20101203 14:04:43| Background correcting data set...
> 20101203 14:04:44|  Already background corrected for "optical" effects
> 20101203 14:04:44| Background correcting data set...done
> 20101203 14:04:44| Estimating specific binding parameters (data
> dependent)...
> 20101203 14:04:44|  Extracting PM indices...
> 20101203 14:04:44|   Reading cell indices from CDF file...
> 20101203 14:04:44|    Pathname:
> annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
> 20101203 14:04:44|    Units:
>      NULL
> 20101203 14:04:44|    lapplyInChunks()...
> 20101203 14:04:44|     Number of elements per chunk: 1e+05
> 20101203 14:04:44|     Chunk #1 of 3...
> 20101203 14:04:44|      Elements:
>        int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
> 20101203 14:04:44|      Querying CDF file...
> 20101203 14:05:08|      Querying CDF file...done
> 20101203 14:05:08|      Restructuring...
> 20101203 14:05:08|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb) max used  (Mb)
>       Ncells  5354837 143.0    6193578 165.4  5373715 143.5
>       Vcells 13471411 102.8   20149605 153.8 13475095 102.9
> 20101203 14:05:09|     Chunk #1 of 3...done
> 20101203 14:05:09|     Chunk #2 of 3...
> 20101203 14:05:09|      Elements:
>        int [1:100000] 100001 100002 100003 100004 100005 100006 100007
> 100008 100009 100010 ...
> 20101203 14:05:09|      Querying CDF file...
> 20101203 14:05:15|      Querying CDF file...done
> 20101203 14:05:15|      Restructuring...
> 20101203 14:05:15|      Restructuring...done
>                  used (Mb) gc trigger  (Mb) max used  (Mb)
>       Ncells  1491395 39.9    4954862 132.4  6193578 165.4
>       Vcells 10685280 81.6   20149605 153.8 17357812 132.5
> 20101203 14:05:16|     Chunk #2 of 3...done
> 20101203 14:05:16|     Chunk #3 of 3...
> 20101203 14:05:16|      Elements:
>        int [1:97051] 200001 200002 200003 200004 200005 200006 200007 200008
> 200009 200010 ...
> 20101203 14:05:16|      Querying CDF file...
> 20101203 14:05:20|      Querying CDF file...done
> 20101203 14:05:21|      Restructuring...
> 20101203 14:05:21|      Restructuring...done
>                  used (Mb) gc trigger  (Mb) max used  (Mb)
>       Ncells  1471326 39.3    4954862 132.4  6193578 165.4
>       Vcells 10882001 83.1   20149605 153.8 17357812 132.5
> 20101203 14:05:21|     Chunk #3 of 3...done
> 20101203 14:05:21|    lapplyInChunks()...done
> 20101203 14:05:21|   Reading cell indices from CDF file...done
>              used (Mb) gc trigger  (Mb) max used  (Mb)
>    Ncells  336599  9.0    3963889 105.9  6193578 165.4
>    Vcells 9592574 73.2   20149605 153.8 17357812 132.5
> 20101203 14:05:21|   readUnits.AffymetrixCdfFile(): Updating cache
> 20101203 14:05:49|  Extracting PM indices...done
>             used (Mb) gc trigger  (Mb) max used  (Mb)
>   Ncells  336674  9.0    2849399  76.1  6193578 165.4
>   Vcells 7232054 55.2   23577885 179.9 23043337 175.9
> 20101203 14:05:49|  Extracting 25000 random PM intensities across CEL set...
> 20101203 14:05:49|   Array #1 of 4...
> 20101203 14:05:50|   Array #1 of 4...done
> 20101203 14:05:50|   Array #2 of 4...
> 20101203 14:05:50|   Array #2 of 4...done
> 20101203 14:05:50|   Array #3 of 4...
> 20101203 14:05:50|   Array #3 of 4...done
> 20101203 14:05:50|   Array #4 of 4...
> 20101203 14:05:50|   Array #4 of 4...done
>              used (Mb) gc trigger  (Mb) max used  (Mb)
>    Ncells  337074  9.1    2279519  60.9  6193578 165.4
>    Vcells 7257179 55.4   23577885 179.9 23043337 175.9
> 20101203 14:05:50|  Extracting 25000 random PM intensities across CEL
> set...done
> 20101203 14:05:50|  Extracting probe affinities and fitting linear model...
>              used (Mb) gc trigger  (Mb) max used  (Mb)
>    Ncells  337074  9.1    1823615  48.7  6193578 165.4
>    Vcells 7269671 55.5   23577885 179.9 23043337 175.9
> 20101203 14:05:51|   Fitting the GCRMA background linear model...
>      num [1:25000] 6.13 10.17 5.73 7.87 10.87 ...
>      num [1:25000] 0.097 0.771 0.181 0.443 1.88 ...
>
>     Call:
>     lm(formula = pm.random2 ~ aff)
>
>     Coefficients:
>     (Intercept)          aff
>           7.104        0.597
>
> 20101203 14:05:51|   Fitting the GCRMA background linear model...done
> 20101203 14:05:51|  Extracting probe affinities and fitting linear
> model...done
> 20101203 14:05:51|  parametersGsb:
>   (Intercept)         aff
>     7.1042892   0.5969684
> 20101203 14:05:51| Estimating specific binding parameters (data
> dependent)...done
> 20101203 14:05:51| Adjusting 4 arrays...
> 20101203 14:05:51|  Array #1 of 4...
>    AffymetrixCelFile:
>    Name: 10 ZEB1_(HuEx-1_0-st-v2)
>    Tags:
>    Full name: 10 ZEB1_(HuEx-1_0-st-v2)
>    Pathname: probeData/Exon Data,OBC/HuEx-1_0-st-v2/10
> ZEB1_(HuEx-1_0-st-v2).CEL
>    File size: 62.50 MB (65536714 bytes)
>    RAM: 0.00 MB
>    File format: v4 (binary; XDA)
>    Platform: Affymetrix
>    Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>    Timestamp: 2010-12-03 13:43:43
> 20101203 14:05:51|   Retrieving PM and MM signals and affinities...
> 20101203 14:06:26|    Number of PM probes: 5270074
> 20101203 14:06:26|    Number of MM probes: 0
> 20101203 14:06:42|    PM signals:
>      num [1:5270074] 237 480 120 482 421 ...
> 20101203 14:06:42|    MM signals:
>      num(0)
> 20101203 14:06:43|    PM affinities:
>      num [1:5270074] -0.585 -1.687 -1.664 -0.569 1.626 ...
> 20101203 14:06:43|    MM affinities:
>      num(0)
> 20101203 14:06:43|   Retrieving PM and MM signals and affinities...done
> 20101203 14:06:43|   Estimating non-specific binding parameters...
> 20101203 14:06:43|    Model type/flavor: affinities
> 20101203 14:06:43|    Affinity-based GCRMA model background adjustment...
> 20101203 14:06:43|     Using mismatch probes (MMs) as negative controls
> 20101203 14:06:43|     Dropping perfect-match probes (PMs) with missing
> signals or missing affinities...
> 20101203 14:06:43|      Number of finite PMs: 5270074 out of 5270074
> (100.0%)
> 20101203 14:06:43|      Number of finite PM affinities: 5270074 out of
> 5270074 (100.0%)
> 20101203 14:06:44|      Number of PMs kept: 5270074 out of 5270074 (100.0%)
> 20101203 14:06:45|     Dropping perfect-match probes (PMs) with missing
> signals or missing affinities...done
> 20101203 14:06:45|     Dropping negative controls with missing signals or
> missing affinities...
> 20101203 14:06:45|      Number of finite negative controls: 0 out of 0
> (NaN%)
> 20101203 14:06:45|      Number of finite negative-control affinities: 0 out
> of 0 (NaN%)
> 20101203 14:06:45|      Number of negative controls kept: 0 out of 0 (NaN%)
> 20101203 14:06:45|     Dropping negative controls with missing signals or
> missing affinities...done
> 20101203 14:06:45|     Number of PMs: 5270074
> 20101203 14:06:45|     Number of negative controls: 0
> Error in if (from == to) rep.int(from, length.out) else as.vector(c(from,
>  :
>   missing value where TRUE/FALSE needed
> 20101203 14:06:49|  Array #1 of 4...done
> 20101203 14:06:49| Adjusting 4 arrays...done
> 20101203 14:06:49|Background correcting data set...done
>
> Please help me in this regard. Also The passing of cdf and ptf arguments in
> process() is just the trial-error I was trying. I am really sorry for that
> and should have given you the code I have.
> Yours Faithfully,
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
> On Fri, Dec 3, 2010 at 2:50 AM, Henrik Bengtsson
> <[hidden email]> wrote:
>>
>> Hi.
>>
>> On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee
>> <[hidden email]> wrote:
>> > Respected Dr Bengtsson,
>> > I have the following codes and outputs:
>> >> source("http://aroma-project.org/hbLite.R");
>> >> hbInstall("aroma.affymetrix")
>>
>> I'll assume that you've run this recently so that you have
>> aroma.affymetrix v1.8.0 installed, because then you can do what I
>> explain next.  FYI, whenever you get an error, please report what
>> sessionInfo() gives so we can be sure you're up-to-date.
>>
>> Go to the HuEx-1_0-st-v2 chip type page:
>>
>>   http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/
>>
>> and download the Aroma Cell Sequence (ACS) file.  Place it in
>> annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is).  Don't
>> forget to gunzip.
>>
>> You can drop/move/leave the probe-tab file; it won't be needed anymore.
>>
>> The following script should do:
>>
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data";
>> chipType <- "HuEx-1_0-st-v2";
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
>> print(cdf);
>>
>> # Assert that the ACS file is available (not really needed to be done)
>> acs <- getAromaCellSequenceFile(cdf);
>> print(acs);
>>
>> # GCRMA background correction
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> print(bc);
>> csB <- process(bc, verbose=verbose);
>> print(csB);
>>
>> Finally, I've noticed that you've tried to pass arguments 'cdf' and
>> 'ptf' to process(), i.e.
>>
>> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose);
>>
>> That is not correct.  Was that suggested to you anywhere, or is it
>> just part of your trial-and-error?
>>
>> Let me know if this solves your problem
>>
>> /Henrik
>>
>> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> dataSet <- "Exon Data"
>> >> chipType <- "HuEx-1_0-st-v2"
>> >> cdf <-
>> >> AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
>> >> print(cdf)
>> > AffymetrixCdfFile:
>> > Path: annotationData/chipTypes/HuEx-1_0-st-v2
>> > Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
>> > Filesize: 203.31MB
>> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > RAM: 0.00MB
>> > File format: v4 (binary; XDA)
>> > Dimension: 2560x2560
>> > Number of cells: 6553600
>> > Number of units: 297051
>> > Cells per unit: 22.06
>> > Number of QC units: 1
>> >> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
>> >> print(ptf)
>> > AffymetrixProbeTabFile:
>> > Name: HuEx-1_0-st-v2
>> > Tags:
>> > Full name: HuEx-1_0-st-v2
>> > Pathname:
>> > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>> > File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
>> > Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>> > Filesize: 38.25MB
>> > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>> > RAM: 0.00MB
>> > File format: v4 (binary; XDA)
>> > Dimension: 2560x2560
>> > Number of cells: 6553600
>> > Number of units: 18708
>> > Cells per unit: 350.31
>> > Number of QC units: 1
>> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
>> >> print(csR)
>> > AffymetrixCelSet:
>> > Name: Exon Data
>> > Tags:
>> > Path: rawData/Exon Data/HuEx-1_0-st-v2
>> > Platform: Affymetrix
>> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > Number of arrays: 17
>> > Names: 10_5N, 11_6T, ..., 9_5T
>> > Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
>> > Total file size: 1081.22MB
>> > RAM: 0.02MB
>> >> 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: 17 (1081.22MB)
>> > Platform: Affymetrix
>> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > 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/HuEx-1_0-st-v2
>> > Is done: FALSE
>> > RAM: 0.00MB
>> >> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
>> > 20101202 14:46:02|Background correcting data set...
>> > 20101202 14:46:02| Computing probe affinities (independent of data)...
>> > 20101202 14:46:03|  Computing GCRMA probe affinities...
>> > 20101202 14:46:03|   Chip type: HuEx-1_0-st-v2
>> > 20101202 14:46:03|   Number of units: 297051
>> > 20101202 14:46:03|   Locating the cell sequence annotation data file...
>> > 20101202 14:46:03|   Locating the cell sequence annotation data
>> > file...done
>> > 20101202 14:46:03|  Computing GCRMA probe affinities...done
>> > 20101202 14:46:03|  Computing GCRMA probe affinities...
>> > 20101202 14:46:03|   Number of units: 297051
>> > 20101202 14:46:03|   Identify PMs and MMs among the CDF cell indices...
>> >      logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >        Mode    TRUE    NA's
>> >     logical 5270074       0
>> > 20101202 14:46:52|    MMs are defined as non-PMs
>> > 20101202 14:46:52|    Number of PMs: 5270074
>> > 20101202 14:46:52|    Number of MMs: 0
>> > 20101202 14:46:52|   Identify PMs and MMs among the CDF cell
>> > indices...done
>> > 20101202 14:46:52|   Reading probe-sequence data...
>> > 20101202 14:46:52|    Retrieving probe-sequence data...
>> > 20101202 14:46:52|     Chip type (full):
>> > HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > 20101202 14:46:52|     Locating probe-tab file...
>> > 20101202 14:46:52|      Chip type: HuEx-1_0-st-v2
>> >       AffymetrixProbeTabFile:
>> >       Name: HuEx-1_0-st-v2
>> >       Tags:
>> >       Full name: HuEx-1_0-st-v2
>> >       Pathname:
>> > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>> >       File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
>> >       Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>> >       Filesize: 38.25MB
>> >       Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>> >       RAM: 0.00MB
>> >       File format: v4 (binary; XDA)
>> >       Dimension: 2560x2560
>> >       Number of cells: 6553600
>> >       Number of units: 18708
>> >       Cells per unit: 350.31
>> >       Number of QC units: 1
>> > 20101202 14:46:52|     Locating probe-tab file...done
>> > 20101202 14:46:52|     Validating probe-tab file against CDF...
>> > 20101202 14:46:52|      Number of records read: 1
>> > 20101202 14:46:52|      Data read:
>> >       'data.frame': 1 obs. of  1 variable:
>> >        $ probeSetID: chr "2315101"
>> >        - attr(*, "fileHeader")=List of 6
>> >         ..$ comments: NULL
>> >         ..$ sep     : chr "\t"
>> >         ..$ quote   : chr "\""
>> >         ..$ skip    : num 0
>> >         ..$ topRows :List of 10
>> >         .. ..$ : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
>> >         .. ..$ : chr  "494998" "2315101" "917" "193" ...
>> >         .. ..$ : chr  "1734213" "2315101" "1092" "677" ...
>> >         .. ..$ : chr  "4767517" "2315101" "796" "1862" ...
>> >         .. ..$ : chr  "4286427" "2315101" "986" "1674" ...
>> >         .. ..$ : chr  "5760145" "2315102" "144" "2250" ...
>> >         .. ..$ : chr  "671410" "2315102" "689" "262" ...
>> >         .. ..$ : chr  "4275780" "2315102" "579" "1670" ...
>> >         .. ..$ : chr  "4293462" "2315102" "341" "1677" ...
>> >         .. ..$ : chr  "5388" "2315103" "267" "2" ...
>> >         ..$ columns : chr  "Probe ID" "Probe Set ID" "probe x" "probe y"
>> > ...
>> > 20101202 14:46:52|      Unit name:
>> >        chr "2315101"
>> > 20101202 14:46:55|      Unit index: NA
>> > Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` =
>> > <environment>,  :
>> >
>> > [2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit
>> > name
>> > '2315101':
>> > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>> >   at throw(Exception(...))
>> >   at throw.default("Failed to identify CDF unit with unit name '",
>> > unitNa
>> >   at throw("Failed to identify CDF unit with unit name '", unitName, "':
>> >   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/HuEx-1_0-st-v2",
>> >   at do.call("bgAdjustGcrma", args = args)
>> >   at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
>> >   at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
>> > 20101202 14:46:55|     Validating probe-tab file against CDF...done
>> > 20101202 14:46:55|    Retrieving probe-sequence data...done
>> > 20101202 14:46:55|   Reading probe-sequence data...done
>> > 20101202 14:46:55|  Computing GCRMA probe affinities...done
>> > 20101202 14:46:55| Computing probe affinities (independent of
>> > data)...done
>> > 20101202 14:46:55|Background correcting data set...done
>> >
>> > Could you please tell me how to rectify the error?
>> > Thank you.
>> > Prithish Banerjee,
>> > Graduate Research Assistant,
>> > Department of Statistics,
>> > West Virginia University.
>> >
>> > --
>> > 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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> 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 Regarding GCRMA Human Exon.

Prithish Banerjee
Respected Dr Bengtsson,

Thank you very much for your help. It fixed the error and ran the GCRMA for human exon arrays. Thank you again for your help and support.

Yours Faithfully,

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

On Fri, Dec 3, 2010 at 8:45 PM, Henrik Bengtsson <[hidden email]> wrote:
Hi,

sorry, it turns out that you also have to use the unsupported CDF for
the GCRMA step.  It is only needed for that step, hence the setCdf():s
set & undo.  You can download a binary version of HuEx-1_0-st-v2.cdf
at:
Then do:

library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);

dataSet <- "Exon Data";
chipType <- "HuEx-1_0-st-v2";

# The unsupported CDF
cdfS <- AffymetrixCdfFile$byChipType(chipType);
print(cdfS);

# The custom CDF
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
print(cdf);

# Setup data set
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);

# GCRMA background correction
setCdf(csR, cdfS); # Set temporarily
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
setCdf(csR, cdf); # Undo.
setCdf(csB, cdf); # Undo.
print(csB);

That should do it.

FYI, when doing AffymetrixCelSet$byName(...) specify either argument
'chipType' or 'cdf' - not both.

/Henrik

On Fri, Dec 3, 2010 at 11:22 AM, Prithish Banerjee
<[hidden email]> wrote:
> Respected Dr Bengtsson,
> Thank you for your help. Sorry for not providing the sessionInfo() last
> time. I am using aroma.affymetrix v 1.8.0. It solved that error but I am
> facing a new error this time. The sessionInfo and the outputs are as
> follows:
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 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_1.8.0 aroma.apd_0.1.7        affxparser_1.22.0
>  [4] R.huge_0.2.0           aroma.core_1.8.0       aroma.light_1.18.2
>  [7] matrixStats_0.2.2      R.rsp_0.4.0            R.filesets_0.9.1
> [10] digest_0.4.2           R.cache_0.3.0          R.utils_1.5.8
> [13] R.oo_1.7.4             R.methodsS3_1.2.1
> loaded via a namespace (and not attached):
> [1] affy_1.28.0           affyio_1.18.0         Biobase_2.10.0
> [4] Biostrings_2.18.0     gcrma_2.22.0          IRanges_1.8.2
> [7] preprocessCore_1.12.0 splines_2.12.0        tools_2.12.0
>
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.cn")
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data"
>> chipType <- "HuEx-1_0-st-v2"
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
>> print(cdf)
>> acs<-getAromaCellSequenceFile(cdf)
>> print(acs)
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
>> 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: 4 (251.42MB)
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> 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/HuEx-1_0-st-v2
> Is done: FALSE
> RAM: 0.00MB
>> csB <- process(bc, verbose=verbose)
> 20101203 14:04:42|Background correcting data set...
> 20101203 14:04:42| Computing probe affinities (independent of data)...
> 20101203 14:04:42|  Computing GCRMA probe affinities...
> 20101203 14:04:42|   Chip type: HuEx-1_0-st-v2
> 20101203 14:04:42|   Number of units: 297051
> 20101203 14:04:43|   Cached results found.
> 20101203 14:04:43|  Computing GCRMA probe affinities...done
> 20101203 14:04:43|  RAM: 50.00MB
> 20101203 14:04:43| Computing probe affinities (independent of data)...done
> 20101203 14:04:43| Background correcting data set...
> 20101203 14:04:44|  Already background corrected for "optical" effects
> 20101203 14:04:44| Background correcting data set...done
> 20101203 14:04:44| Estimating specific binding parameters (data
> dependent)...
> 20101203 14:04:44|  Extracting PM indices...
> 20101203 14:04:44|   Reading cell indices from CDF file...
> 20101203 14:04:44|    Pathname:
> annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
> 20101203 14:04:44|    Units:
>      NULL
> 20101203 14:04:44|    lapplyInChunks()...
> 20101203 14:04:44|     Number of elements per chunk: 1e+05
> 20101203 14:04:44|     Chunk #1 of 3...
> 20101203 14:04:44|      Elements:
>        int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
> 20101203 14:04:44|      Querying CDF file...
> 20101203 14:05:08|      Querying CDF file...done
> 20101203 14:05:08|      Restructuring...
> 20101203 14:05:08|      Restructuring...done
>                  used  (Mb) gc trigger  (Mb) max used  (Mb)
>       Ncells  5354837 143.0    6193578 165.4  5373715 143.5
>       Vcells 13471411 102.8   20149605 153.8 13475095 102.9
> 20101203 14:05:09|     Chunk #1 of 3...done
> 20101203 14:05:09|     Chunk #2 of 3...
> 20101203 14:05:09|      Elements:
>        int [1:100000] 100001 100002 100003 100004 100005 100006 100007
> 100008 100009 100010 ...
> 20101203 14:05:09|      Querying CDF file...
> 20101203 14:05:15|      Querying CDF file...done
> 20101203 14:05:15|      Restructuring...
> 20101203 14:05:15|      Restructuring...done
>                  used (Mb) gc trigger  (Mb) max used  (Mb)
>       Ncells  1491395 39.9    4954862 132.4  6193578 165.4
>       Vcells 10685280 81.6   20149605 153.8 17357812 132.5
> 20101203 14:05:16|     Chunk #2 of 3...done
> 20101203 14:05:16|     Chunk #3 of 3...
> 20101203 14:05:16|      Elements:
>        int [1:97051] 200001 200002 200003 200004 200005 200006 200007 200008
> 200009 200010 ...
> 20101203 14:05:16|      Querying CDF file...
> 20101203 14:05:20|      Querying CDF file...done
> 20101203 14:05:21|      Restructuring...
> 20101203 14:05:21|      Restructuring...done
>                  used (Mb) gc trigger  (Mb) max used  (Mb)
>       Ncells  1471326 39.3    4954862 132.4  6193578 165.4
>       Vcells 10882001 83.1   20149605 153.8 17357812 132.5
> 20101203 14:05:21|     Chunk #3 of 3...done
> 20101203 14:05:21|    lapplyInChunks()...done
> 20101203 14:05:21|   Reading cell indices from CDF file...done
>              used (Mb) gc trigger  (Mb) max used  (Mb)
>    Ncells  336599  9.0    3963889 105.9  6193578 165.4
>    Vcells 9592574 73.2   20149605 153.8 17357812 132.5
> 20101203 14:05:21|   readUnits.AffymetrixCdfFile(): Updating cache
> 20101203 14:05:49|  Extracting PM indices...done
>             used (Mb) gc trigger  (Mb) max used  (Mb)
>   Ncells  336674  9.0    2849399  76.1  6193578 165.4
>   Vcells 7232054 55.2   23577885 179.9 23043337 175.9
> 20101203 14:05:49|  Extracting 25000 random PM intensities across CEL set...
> 20101203 14:05:49|   Array #1 of 4...
> 20101203 14:05:50|   Array #1 of 4...done
> 20101203 14:05:50|   Array #2 of 4...
> 20101203 14:05:50|   Array #2 of 4...done
> 20101203 14:05:50|   Array #3 of 4...
> 20101203 14:05:50|   Array #3 of 4...done
> 20101203 14:05:50|   Array #4 of 4...
> 20101203 14:05:50|   Array #4 of 4...done
>              used (Mb) gc trigger  (Mb) max used  (Mb)
>    Ncells  337074  9.1    2279519  60.9  6193578 165.4
>    Vcells 7257179 55.4   23577885 179.9 23043337 175.9
> 20101203 14:05:50|  Extracting 25000 random PM intensities across CEL
> set...done
> 20101203 14:05:50|  Extracting probe affinities and fitting linear model...
>              used (Mb) gc trigger  (Mb) max used  (Mb)
>    Ncells  337074  9.1    1823615  48.7  6193578 165.4
>    Vcells 7269671 55.5   23577885 179.9 23043337 175.9
> 20101203 14:05:51|   Fitting the GCRMA background linear model...
>      num [1:25000] 6.13 10.17 5.73 7.87 10.87 ...
>      num [1:25000] 0.097 0.771 0.181 0.443 1.88 ...
>
>     Call:
>     lm(formula = pm.random2 ~ aff)
>
>     Coefficients:
>     (Intercept)          aff
>           7.104        0.597
>
> 20101203 14:05:51|   Fitting the GCRMA background linear model...done
> 20101203 14:05:51|  Extracting probe affinities and fitting linear
> model...done
> 20101203 14:05:51|  parametersGsb:
>   (Intercept)         aff
>     7.1042892   0.5969684
> 20101203 14:05:51| Estimating specific binding parameters (data
> dependent)...done
> 20101203 14:05:51| Adjusting 4 arrays...
> 20101203 14:05:51|  Array #1 of 4...
>    AffymetrixCelFile:
>    Name: 10 ZEB1_(HuEx-1_0-st-v2)
>    Tags:
>    Full name: 10 ZEB1_(HuEx-1_0-st-v2)
>    Pathname: probeData/Exon Data,OBC/HuEx-1_0-st-v2/10
> ZEB1_(HuEx-1_0-st-v2).CEL
>    File size: 62.50 MB (65536714 bytes)
>    RAM: 0.00 MB
>    File format: v4 (binary; XDA)
>    Platform: Affymetrix
>    Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>    Timestamp: 2010-12-03 13:43:43
> 20101203 14:05:51|   Retrieving PM and MM signals and affinities...
> 20101203 14:06:26|    Number of PM probes: 5270074
> 20101203 14:06:26|    Number of MM probes: 0
> 20101203 14:06:42|    PM signals:
>      num [1:5270074] 237 480 120 482 421 ...
> 20101203 14:06:42|    MM signals:
>      num(0)
> 20101203 14:06:43|    PM affinities:
>      num [1:5270074] -0.585 -1.687 -1.664 -0.569 1.626 ...
> 20101203 14:06:43|    MM affinities:
>      num(0)
> 20101203 14:06:43|   Retrieving PM and MM signals and affinities...done
> 20101203 14:06:43|   Estimating non-specific binding parameters...
> 20101203 14:06:43|    Model type/flavor: affinities
> 20101203 14:06:43|    Affinity-based GCRMA model background adjustment...
> 20101203 14:06:43|     Using mismatch probes (MMs) as negative controls
> 20101203 14:06:43|     Dropping perfect-match probes (PMs) with missing
> signals or missing affinities...
> 20101203 14:06:43|      Number of finite PMs: 5270074 out of 5270074
> (100.0%)
> 20101203 14:06:43|      Number of finite PM affinities: 5270074 out of
> 5270074 (100.0%)
> 20101203 14:06:44|      Number of PMs kept: 5270074 out of 5270074 (100.0%)
> 20101203 14:06:45|     Dropping perfect-match probes (PMs) with missing
> signals or missing affinities...done
> 20101203 14:06:45|     Dropping negative controls with missing signals or
> missing affinities...
> 20101203 14:06:45|      Number of finite negative controls: 0 out of 0
> (NaN%)
> 20101203 14:06:45|      Number of finite negative-control affinities: 0 out
> of 0 (NaN%)
> 20101203 14:06:45|      Number of negative controls kept: 0 out of 0 (NaN%)
> 20101203 14:06:45|     Dropping negative controls with missing signals or
> missing affinities...done
> 20101203 14:06:45|     Number of PMs: 5270074
> 20101203 14:06:45|     Number of negative controls: 0
> Error in if (from == to) rep.int(from, length.out) else as.vector(c(from,
>  :
>   missing value where TRUE/FALSE needed
> 20101203 14:06:49|  Array #1 of 4...done
> 20101203 14:06:49| Adjusting 4 arrays...done
> 20101203 14:06:49|Background correcting data set...done
>
> Please help me in this regard. Also The passing of cdf and ptf arguments in
> process() is just the trial-error I was trying. I am really sorry for that
> and should have given you the code I have.
> Yours Faithfully,
> Prithish Banerjee,
> Graduate Research Assistant,
> Department of Statistics,
> West Virginia University.
> On Fri, Dec 3, 2010 at 2:50 AM, Henrik Bengtsson
> <[hidden email]> wrote:
>>
>> Hi.
>>
>> On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee
>> <[hidden email]> wrote:
>> > Respected Dr Bengtsson,
>> > I have the following codes and outputs:
>> >> source("http://aroma-project.org/hbLite.R");
>> >> hbInstall("aroma.affymetrix")
>>
>> I'll assume that you've run this recently so that you have
>> aroma.affymetrix v1.8.0 installed, because then you can do what I
>> explain next.  FYI, whenever you get an error, please report what
>> sessionInfo() gives so we can be sure you're up-to-date.
>>
>> Go to the HuEx-1_0-st-v2 chip type page:
>>
>>   http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/
>>
>> and download the Aroma Cell Sequence (ACS) file.  Place it in
>> annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is).  Don't
>> forget to gunzip.
>>
>> You can drop/move/leave the probe-tab file; it won't be needed anymore.
>>
>> The following script should do:
>>
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> dataSet <- "Exon Data";
>> chipType <- "HuEx-1_0-st-v2";
>> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
>> print(cdf);
>>
>> # Assert that the ACS file is available (not really needed to be done)
>> acs <- getAromaCellSequenceFile(cdf);
>> print(acs);
>>
>> # GCRMA background correction
>> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>> print(bc);
>> csB <- process(bc, verbose=verbose);
>> print(csB);
>>
>> Finally, I've noticed that you've tried to pass arguments 'cdf' and
>> 'ptf' to process(), i.e.
>>
>> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose);
>>
>> That is not correct.  Was that suggested to you anywhere, or is it
>> just part of your trial-and-error?
>>
>> Let me know if this solves your problem
>>
>> /Henrik
>>
>> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>> >> dataSet <- "Exon Data"
>> >> chipType <- "HuEx-1_0-st-v2"
>> >> cdf <-
>> >> AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
>> >> print(cdf)
>> > AffymetrixCdfFile:
>> > Path: annotationData/chipTypes/HuEx-1_0-st-v2
>> > Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
>> > Filesize: 203.31MB
>> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > RAM: 0.00MB
>> > File format: v4 (binary; XDA)
>> > Dimension: 2560x2560
>> > Number of cells: 6553600
>> > Number of units: 297051
>> > Cells per unit: 22.06
>> > Number of QC units: 1
>> >> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
>> >> print(ptf)
>> > AffymetrixProbeTabFile:
>> > Name: HuEx-1_0-st-v2
>> > Tags:
>> > Full name: HuEx-1_0-st-v2
>> > Pathname:
>> > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>> > File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
>> > Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>> > Filesize: 38.25MB
>> > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>> > RAM: 0.00MB
>> > File format: v4 (binary; XDA)
>> > Dimension: 2560x2560
>> > Number of cells: 6553600
>> > Number of units: 18708
>> > Cells per unit: 350.31
>> > Number of QC units: 1
>> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
>> >> print(csR)
>> > AffymetrixCelSet:
>> > Name: Exon Data
>> > Tags:
>> > Path: rawData/Exon Data/HuEx-1_0-st-v2
>> > Platform: Affymetrix
>> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > Number of arrays: 17
>> > Names: 10_5N, 11_6T, ..., 9_5T
>> > Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
>> > Total file size: 1081.22MB
>> > RAM: 0.02MB
>> >> 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: 17 (1081.22MB)
>> > Platform: Affymetrix
>> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > 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/HuEx-1_0-st-v2
>> > Is done: FALSE
>> > RAM: 0.00MB
>> >> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
>> > 20101202 14:46:02|Background correcting data set...
>> > 20101202 14:46:02| Computing probe affinities (independent of data)...
>> > 20101202 14:46:03|  Computing GCRMA probe affinities...
>> > 20101202 14:46:03|   Chip type: HuEx-1_0-st-v2
>> > 20101202 14:46:03|   Number of units: 297051
>> > 20101202 14:46:03|   Locating the cell sequence annotation data file...
>> > 20101202 14:46:03|   Locating the cell sequence annotation data
>> > file...done
>> > 20101202 14:46:03|  Computing GCRMA probe affinities...done
>> > 20101202 14:46:03|  Computing GCRMA probe affinities...
>> > 20101202 14:46:03|   Number of units: 297051
>> > 20101202 14:46:03|   Identify PMs and MMs among the CDF cell indices...
>> >      logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
>> >        Mode    TRUE    NA's
>> >     logical 5270074       0
>> > 20101202 14:46:52|    MMs are defined as non-PMs
>> > 20101202 14:46:52|    Number of PMs: 5270074
>> > 20101202 14:46:52|    Number of MMs: 0
>> > 20101202 14:46:52|   Identify PMs and MMs among the CDF cell
>> > indices...done
>> > 20101202 14:46:52|   Reading probe-sequence data...
>> > 20101202 14:46:52|    Retrieving probe-sequence data...
>> > 20101202 14:46:52|     Chip type (full):
>> > HuEx-1_0-st-v2,fullR3,A20071112,EP
>> > 20101202 14:46:52|     Locating probe-tab file...
>> > 20101202 14:46:52|      Chip type: HuEx-1_0-st-v2
>> >       AffymetrixProbeTabFile:
>> >       Name: HuEx-1_0-st-v2
>> >       Tags:
>> >       Full name: HuEx-1_0-st-v2
>> >       Pathname:
>> > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>> >       File size: 527.80 MB (553438704 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/HuEx-1_0-st-v2
>> >       Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>> >       Filesize: 38.25MB
>> >       Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>> >       RAM: 0.00MB
>> >       File format: v4 (binary; XDA)
>> >       Dimension: 2560x2560
>> >       Number of cells: 6553600
>> >       Number of units: 18708
>> >       Cells per unit: 350.31
>> >       Number of QC units: 1
>> > 20101202 14:46:52|     Locating probe-tab file...done
>> > 20101202 14:46:52|     Validating probe-tab file against CDF...
>> > 20101202 14:46:52|      Number of records read: 1
>> > 20101202 14:46:52|      Data read:
>> >       'data.frame': 1 obs. of  1 variable:
>> >        $ probeSetID: chr "2315101"
>> >        - attr(*, "fileHeader")=List of 6
>> >         ..$ comments: NULL
>> >         ..$ sep     : chr "\t"
>> >         ..$ quote   : chr "\""
>> >         ..$ skip    : num 0
>> >         ..$ topRows :List of 10
>> >         .. ..$ : chr  "Probe ID" "Probe Set ID" "probe x" "probe y" ...
>> >         .. ..$ : chr  "494998" "2315101" "917" "193" ...
>> >         .. ..$ : chr  "1734213" "2315101" "1092" "677" ...
>> >         .. ..$ : chr  "4767517" "2315101" "796" "1862" ...
>> >         .. ..$ : chr  "4286427" "2315101" "986" "1674" ...
>> >         .. ..$ : chr  "5760145" "2315102" "144" "2250" ...
>> >         .. ..$ : chr  "671410" "2315102" "689" "262" ...
>> >         .. ..$ : chr  "4275780" "2315102" "579" "1670" ...
>> >         .. ..$ : chr  "4293462" "2315102" "341" "1677" ...
>> >         .. ..$ : chr  "5388" "2315103" "267" "2" ...
>> >         ..$ columns : chr  "Probe ID" "Probe Set ID" "probe x" "probe y"
>> > ...
>> > 20101202 14:46:52|      Unit name:
>> >        chr "2315101"
>> > 20101202 14:46:55|      Unit index: NA
>> > Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` =
>> > <environment>,  :
>> >
>> > [2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit
>> > name
>> > '2315101':
>> > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
>> >   at throw(Exception(...))
>> >   at throw.default("Failed to identify CDF unit with unit name '",
>> > unitNa
>> >   at throw("Failed to identify CDF unit with unit name '", unitName, "':
>> >   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/HuEx-1_0-st-v2",
>> >   at do.call("bgAdjustGcrma", args = args)
>> >   at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
>> >   at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
>> > 20101202 14:46:55|     Validating probe-tab file against CDF...done
>> > 20101202 14:46:55|    Retrieving probe-sequence data...done
>> > 20101202 14:46:55|   Reading probe-sequence data...done
>> > 20101202 14:46:55|  Computing GCRMA probe affinities...done
>> > 20101202 14:46:55| Computing probe affinities (independent of
>> > data)...done
>> > 20101202 14:46:55|Background correcting data set...done
>> >
>> > Could you please tell me how to rectify the error?
>> > Thank you.
>> > Prithish Banerjee,
>> > Graduate Research Assistant,
>> > Department of Statistics,
>> > West Virginia University.
>> >
>> > --
>> > 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]
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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.
 
 
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