[aroma.affymetrix] Error: object 'csC' not found.

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[aroma.affymetrix] Error: object 'csC' not found.

wxpyzr
Hi dear professor   Henrik Bengtsson,

When I was declaring the raw data set of CytoScan HD Array with aroma.affymetrix, I'm encountering the following errors: 

"Error: object 'csC' not found." 

I have searched the forum, unfortunately, I can't solve this problem.

Could you give me some suggestions and help me solve it ?

The following are the R code of mine:

> setwd("G:/")

>library("aroma.affymetrix")

>log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)

>options(digits=4)

>cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")

>gi <- getGenomeInformation(cdf)

>si <- getSnpInformation(cdf)

>acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))

>csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)

>acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")

>csC <- process(acc, verbose=verbose)

print(csC)

> sessionInfo() 
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] aroma.light_2.4.0       aroma.affymetrix_2.14.0 affxparser_1.42.0      
[4] aroma.core_3.0.0        R.devices_2.13.2        R.filesets_2.10.0      
[7] R.utils_2.2.0           R.oo_1.19.0             R.methodsS3_1.7.0      

loaded via a namespace (and not attached):

 [1] matrixStats_0.50.1 codetools_0.2-14   listenv_0.6.0      future_0.10.0     
 [5] digest_0.6.8       R.huge_0.9.0       PSCBS_0.60.0       tools_3.2.2       
 [9] R.cache_0.12.0     parallel_3.2.2     base64enc_0.1-3    aroma.apd_0.6.0   
[13] R.rsp_0.21.0       globals_0.6.0      DNAcopy_1.42.0    

CEL format raw data are locate in "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"

Looking forward your replay. Thank you very much.








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Re: [aroma.affymetrix] Error: object 'csC' not found.

Henrik Bengtsson-2
On Sun, Jan 10, 2016 at 11:36 PM, <[hidden email]> wrote:
>
> Hi dear professor   Henrik Bengtsson,
>
> When I was declaring the raw data set of CytoScan HD Array with aroma.affymetrix, I'm encountering the following errors:
>
> "Error: object 'csC' not found."

It seems like you didn't run the command before.  Make sure each
object is actually created in every step by printing it, e.g.
print(cdf), etc.  That should help you narrow down where your problem
is.

/Henrik

>
> I have searched the forum, unfortunately, I can't solve this problem.
>
> Could you give me some suggestions and help me solve it ?
>
> The following are the R code of mine:
>
> > setwd("G:/")
>
> >library("aroma.affymetrix")
>
> >log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> >options(digits=4)
>
> >cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
>
> >gi <- getGenomeInformation(cdf)
>
> >si <- getSnpInformation(cdf)
>
> >acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))
>
> >csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)
>
> >acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>
> >csC <- process(acc, verbose=verbose)
>
> > print(csC)
>
> > sessionInfo()
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] aroma.light_2.4.0       aroma.affymetrix_2.14.0 affxparser_1.42.0
> [4] aroma.core_3.0.0        R.devices_2.13.2        R.filesets_2.10.0
> [7] R.utils_2.2.0           R.oo_1.19.0             R.methodsS3_1.7.0
>
> loaded via a namespace (and not attached):
>
>  [1] matrixStats_0.50.1 codetools_0.2-14   listenv_0.6.0      future_0.10.0
>  [5] digest_0.6.8       R.huge_0.9.0       PSCBS_0.60.0       tools_3.2.2
>  [9] R.cache_0.12.0     parallel_3.2.2     base64enc_0.1-3    aroma.apd_0.6.0
> [13] R.rsp_0.21.0       globals_0.6.0      DNAcopy_1.42.0
>
> CEL format raw data are locate in "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"
>
> Looking forward your replay. Thank you very much.
>
>
>
>
>
>
>
>
> --
> --
> 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/
>
> ---
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
> For more options, visit https://groups.google.com/d/optout.

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


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

---
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Re: [aroma.affymetrix] Error: object 'csC' not found.

Wulc
This post has NOT been accepted by the mailing list yet.
Dear professor Henrik Bengtsson

Many thanks for your replay.

Actually, when I  created the object csC with the following code:

csC <- process(acc, verbose=verbose)

I encountered the Error: length(uPos) > 0 is not TRUE;

That's why the object 'csC' not found.

######################################

the following are the output content
> csC <- process(acc, verbose=verbose)
20160118 00:37:14|Calibrating data set for allelic cross talk...
20160118 00:37:16| Compressing model parameter to a short format...
20160118 00:37:16| Compressing model parameter to a short format...done
20160118 00:37:16| Calibrating 6 arrays...
20160118 00:37:16|  Path: probeData/cnv,ACC,ra,-XY/CytoScanHD_Array
20160118 00:37:16|  Array #1 ('01') of 6...
20160118 00:37:16|   Identifying sets of pairs of cell indices...
20160118 00:37:16|    Chip type: CytoScanHD_Array
20160118 00:37:17|    Merge shifts: TRUE
20160118 00:37:17|    Number of nucleotides: 1
20160118 00:37:17|    Locating AromaCellSequenceFile...
20160118 00:37:17|     Chip type: CytoScanHD_Array
20160118 00:37:17|     Number of cells: 6892960
     AromaCellSequenceFile:
     Name: CytoScanHD_Array
     Tags:
     Full name: CytoScanHD_Array
     Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array.acs
     File size: 170.92 MiB (179217487 bytes)
     RAM: 0.00 MB
     Number of data rows: 6892960
     File format: v1
     Dimensions: 6892960x26
     Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
     Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
     Footer: <createdOn>20111108 21:44:22 PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik Bengtsson</fullname>[hidden email]</createdBy>
     Chip type: CytoScanHD_Array
     Platform: Affymetrix
20160118 00:37:17|    Locating AromaCellSequenceFile...done
20160118 00:37:17|    Identifying cell indices for all non-SNP units...
20160118 00:37:17|     Non-SNP units:...
       int [1:2020614] 1 2 3 4 5 6 7 8 9 10 ...
20160118 00:37:17|      getCellIndices.AffymetrixCdfFile(): Returning cached data
20160118 00:37:17|      Non-SNP cells:...
        int [1:2037534] 6344052 5132417 3744071 1409905 879528 5837958 5341975 4106306 1391737 1201593 ...
20160118 00:37:17|      Non-SNP cells:...done
20160118 00:37:17|      Identifying the probe pairs...
20160118 00:37:17|       Units:
        NULL
20160118 00:37:17|       Checking for cached results...
20160118 00:37:17|        Found cached results
20160118 00:37:17|       Checking for cached results...done
20160118 00:37:17|      Identifying the probe pairs...done
20160118 00:37:17|      Probe shifts:
      [1] 0
20160118 00:37:17|      Identifying groups of SNP nucleotide sequence pairs...
20160118 00:37:17|       Checking for cached results...
20160118 00:37:17|       Checking for cached results...done
20160118 00:37:17|       Get SNP nucleotide sequence pairs...
20160118 00:37:17|        Retrieving SNP nucleotides...
20160118 00:37:17|         Probe shifts:
          int 0
20160118 00:37:17|         Argument 'cells':
          int [1:2, 1:2410205] 702209 3820208 6174755 2915229 1437029 2981430 4652935 141307 3892235 1614497 ...
          - attr(*, "dimnames")=List of 2
           ..$ : chr [1:2] "A" "B"
           ..$ : NULL
20160118 00:37:17|         Number of pairs: 2410205
20160118 00:37:17|         Identifying SNP positions of cell allele pairs...
20160118 00:37:17|          Checking for cached results...
20160118 00:37:18|           Found cached results
20160118 00:37:18|          Checking for cached results...done
20160118 00:37:18|         Identifying SNP positions of cell allele pairs...done
20160118 00:37:18|         SNP positions:
          int [1:2410205] NA NA NA NA NA NA NA NA NA NA ...
20160118 00:37:18|         Tabulated SNP positions:
         < table of extent 0 >
20160118 00:37:18|         Unique SNP positions:
         integer(0)
Error: length(uPos) > 0 is not TRUE
20160118 00:37:18|        Retrieving SNP nucleotides...done
20160118 00:37:18|       Get SNP nucleotide sequence pairs...done
20160118 00:37:18|      Identifying groups of SNP nucleotide sequence pairs...done
20160118 00:37:18|     Non-SNP units:...done
20160118 00:37:18|    Identifying cell indices for all non-SNP units...done
20160118 00:37:18|   Identifying sets of pairs of cell indices...done
20160118 00:37:18|  Array #1 ('01') of 6...done
20160118 00:37:18| Calibrating 6 arrays...done
20160118 00:37:18|Calibrating data set for allelic cross talk...done
> csC
Error: object 'csC' not found

#########################

the annotation file was down load from
 
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/

However I can't solve this problem.

Could you point out what's the real problem?

Thank you very much!



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Re: [aroma.affymetrix] Error: object 'csC' not found.

ali jan
In reply to this post by Henrik Bengtsson-2
I tried your suggestion but it is still not working:

> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> # Don't display too many decimals.
> options(digits=4)
> cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
File size: 612.27 MiB (642007896 bytes)
Chip type: CytoScanHD_Array
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4
> gi <- getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB20111108
Full name: CytoScanHD_Array,na32,hg19,HB20111108
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ugp
File size: 13.46 MiB (14111425 bytes)
Chip type: CytoScanHD_Array
> si <- getSnpInformation(cdf)
> print(si)
UflSnpInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB20111108
Full name: CytoScanHD_Array,na32,hg19,HB20111108
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ufl
File size: 5.38 MiB (5645047 bytes)
Chip type: CytoScanHD_Array
Number of enzymes: 1
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MiB (179217487 bytes)
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20111108 21:44:22 PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik Bengtsson</fullname><email>[hidden email]</email></createdBy>
Chip type: CytoScanHD_Array
Platform: Affymetrix
> csR <- AffymetrixCelSet$byName("CNV", cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: CNV
Tags: 
Path: rawData/CNV/CytoScanHD_Array
Platform: Affymetrix
Chip type: CytoScanHD_Array
Number of arrays: 460
Names: GSM1317174_H050150N-CytoScanHD_515-H050150N, GSM1317175_H050150T-CytoScanHD_516-H050150T, GSM1317176_H050154N-CytoScanHD_521-H050154N, ..., GSM1317635_H112971T-CytoScanHD_831-H112971T [460]
Time period: 2012-03-12 16:49:41 -- 2012-04-05 08:47:43
Total file size: 29.55 GiB
> cs <- csR
> par(mar=c(4,4,1,1)+0.1)
> plotDensity(cs, lwd=2, ylim=c(0,0.40))

> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> print(acc)
AllelicCrosstalkCalibration:
Data set: CNV
Input tags: 
User tags: *
Asterisk ('*') tags: ACC,ra,-XY
Output tags: ACC,ra,-XY
Number of files: 460 (29.55 GiB)
Platform: Affymetrix
Chip type: CytoScanHD_Array
Algorithm parameters: {rescaleBy: chr "all", targetAvg: num 2200, subsetToAvg: int [1:6538333] 1 2 3 4 5 6 7 8 11 12 ..., mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98}
Output path: probeData/CNV,ACC,ra,-XY/CytoScanHD_Array
Is done: FALSE
> print(csC)
Error in print(csC) : object 'csC' not found
> sessionInfo() 
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] aroma.light_3.8.0      aroma.affymetrix_3.1.0 aroma.core_3.1.1       R.devices_2.15.1       R.filesets_2.11.0      R.utils_2.5.0         
[7] R.oo_1.21.0            affxparser_1.50.0      R.methodsS3_1.7.1     

loaded via a namespace (and not attached):
 [1] matrixStats_0.52.2 codetools_0.2-15   listenv_0.6.0      future_1.6.2       digest_0.6.12      R.huge_0.9.0       PSCBS_0.63.0      
 [8] tools_3.4.2        R.cache_0.12.0     parallel_3.4.2     compiler_3.4.2     base64enc_0.1-3    aroma.apd_0.6.0    R.rsp_0.41.0      
[15] globals_0.10.3     DNAcopy_1.52.0    
> traceback()
No traceback available 

On Wednesday, January 13, 2016 at 11:05:11 PM UTC+5, Henrik Bengtsson wrote:
On Sun, Jan 10, 2016 at 11:36 PM, <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="_eDRl9gREgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wxp...@...> wrote:
>
> Hi dear professor   Henrik Bengtsson,
>
> When I was declaring the raw data set of CytoScan HD Array with aroma.affymetrix, I'm encountering the following errors:
>
> "Error: object 'csC' not found."

It seems like you didn't run the command before.  Make sure each
object is actually created in every step by printing it, e.g.
print(cdf), etc.  That should help you narrow down where your problem
is.

/Henrik

>
> I have searched the forum, unfortunately, I can't solve this problem.
>
> Could you give me some suggestions and help me solve it ?
>
> The following are the R code of mine:
>
> > setwd("G:/")
>
> >library("aroma.affymetrix")
>
> >log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> >options(digits=4)
>
> >cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
>
> >gi <- getGenomeInformation(cdf)
>
> >si <- getSnpInformation(cdf)
>
> >acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))
>
> >csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)
>
> >acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>
> >csC <- process(acc, verbose=verbose)
>
> > print(csC)
>
> > sessionInfo()
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] aroma.light_2.4.0       aroma.affymetrix_2.14.0 affxparser_1.42.0
> [4] aroma.core_3.0.0        R.devices_2.13.2        R.filesets_2.10.0
> [7] R.utils_2.2.0           R.oo_1.19.0             R.methodsS3_1.7.0
>
> loaded via a namespace (and not attached):
>
>  [1] matrixStats_0.50.1 codetools_0.2-14   listenv_0.6.0      future_0.10.0
>  [5] digest_0.6.8       R.huge_0.9.0       PSCBS_0.60.0       tools_3.2.2
>  [9] R.cache_0.12.0     parallel_3.2.2     base64enc_0.1-3    aroma.apd_0.6.0
> [13] R.rsp_0.21.0       globals_0.6.0      DNAcopy_1.42.0
>
> CEL format raw data are locate in "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"
>
> Looking forward your replay. Thank you very much.
>
>
>
>
>
>
>
>
> --
> --
> 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] Error: object 'csC' not found.

321bixin
hello,have you solved your problem? I met the same error

在 2017年11月14日星期二 UTC+8上午8:29:07,ali jan写道:
I tried your suggestion but it is still not working:

> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> # Don't display too many decimals.
> options(digits=4)
> cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
File size: 612.27 MiB (642007896 bytes)
Chip type: CytoScanHD_Array
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4
> gi <- getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB20111108
Full name: CytoScanHD_Array,na32,hg19,HB20111108
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ugp
File size: 13.46 MiB (14111425 bytes)
Chip type: CytoScanHD_Array
> si <- getSnpInformation(cdf)
> print(si)
UflSnpInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB20111108
Full name: CytoScanHD_Array,na32,hg19,HB20111108
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ufl
File size: 5.38 MiB (5645047 bytes)
Chip type: CytoScanHD_Array
Number of enzymes: 1
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MiB (179217487 bytes)
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20111108 21:44:22 PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik Bengtsson</fullname><email><a href="javascript:" target="_blank" gdf-obfuscated-mailto="Iiy3Y5yTCwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">henrik.bengtsson@aroma-project.org</email></createdBy>
Chip type: CytoScanHD_Array
Platform: Affymetrix
> csR <- AffymetrixCelSet$byName("CNV", cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: CNV
Tags: 
Path: rawData/CNV/CytoScanHD_Array
Platform: Affymetrix
Chip type: CytoScanHD_Array
Number of arrays: 460
Names: GSM1317174_H050150N-CytoScanHD_515-H050150N, GSM1317175_H050150T-CytoScanHD_516-H050150T, GSM1317176_H050154N-CytoScanHD_521-H050154N, ..., GSM1317635_H112971T-CytoScanHD_831-H112971T [460]
Time period: 2012-03-12 16:49:41 -- 2012-04-05 08:47:43
Total file size: 29.55 GiB
> cs <- csR
> par(mar=c(4,4,1,1)+0.1)
> plotDensity(cs, lwd=2, ylim=c(0,0.40))

> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> print(acc)
AllelicCrosstalkCalibration:
Data set: CNV
Input tags: 
User tags: *
Asterisk ('*') tags: ACC,ra,-XY
Output tags: ACC,ra,-XY
Number of files: 460 (29.55 GiB)
Platform: Affymetrix
Chip type: CytoScanHD_Array
Algorithm parameters: {rescaleBy: chr "all", targetAvg: num 2200, subsetToAvg: int [1:6538333] 1 2 3 4 5 6 7 8 11 12 ..., mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98}
Output path: probeData/CNV,ACC,ra,-XY/CytoScanHD_Array
Is done: FALSE
> print(csC)
Error in print(csC) : object 'csC' not found
> sessionInfo() 
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] aroma.light_3.8.0      aroma.affymetrix_3.1.0 aroma.core_3.1.1       R.devices_2.15.1       R.filesets_2.11.0      R.utils_2.5.0         
[7] R.oo_1.21.0            affxparser_1.50.0      R.methodsS3_1.7.1     

loaded via a namespace (and not attached):
 [1] matrixStats_0.52.2 codetools_0.2-15   listenv_0.6.0      future_1.6.2       digest_0.6.12      R.huge_0.9.0       PSCBS_0.63.0      
 [8] tools_3.4.2        R.cache_0.12.0     parallel_3.4.2     compiler_3.4.2     base64enc_0.1-3    aroma.apd_0.6.0    R.rsp_0.41.0      
[15] globals_0.10.3     DNAcopy_1.52.0    
> traceback()
No traceback available 

On Wednesday, January 13, 2016 at 11:05:11 PM UTC+5, Henrik Bengtsson wrote:
On Sun, Jan 10, 2016 at 11:36 PM, <[hidden email]> wrote:
>
> Hi dear professor   Henrik Bengtsson,
>
> When I was declaring the raw data set of CytoScan HD Array with aroma.affymetrix, I'm encountering the following errors:
>
> "Error: object 'csC' not found."

It seems like you didn't run the command before.  Make sure each
object is actually created in every step by printing it, e.g.
print(cdf), etc.  That should help you narrow down where your problem
is.

/Henrik

>
> I have searched the forum, unfortunately, I can't solve this problem.
>
> Could you give me some suggestions and help me solve it ?
>
> The following are the R code of mine:
>
> > setwd("G:/")
>
> >library("aroma.affymetrix")
>
> >log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> >options(digits=4)
>
> >cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
>
> >gi <- getGenomeInformation(cdf)
>
> >si <- getSnpInformation(cdf)
>
> >acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))
>
> >csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)
>
> >acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>
> >csC <- process(acc, verbose=verbose)
>
> > print(csC)
>
> > sessionInfo()
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] aroma.light_2.4.0       aroma.affymetrix_2.14.0 affxparser_1.42.0
> [4] aroma.core_3.0.0        R.devices_2.13.2        R.filesets_2.10.0
> [7] R.utils_2.2.0           R.oo_1.19.0             R.methodsS3_1.7.0
>
> loaded via a namespace (and not attached):
>
>  [1] matrixStats_0.50.1 codetools_0.2-14   listenv_0.6.0      future_0.10.0
>  [5] digest_0.6.8       R.huge_0.9.0       PSCBS_0.60.0       tools_3.2.2
>  [9] R.cache_0.12.0     parallel_3.2.2     base64enc_0.1-3    aroma.apd_0.6.0
> [13] R.rsp_0.21.0       globals_0.6.0      DNAcopy_1.42.0
>
> CEL format raw data are locate in "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"
>
> Looking forward your replay. Thank you very much.
>
>
>
>
>
>
>
>
> --
> --
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>
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Re: [aroma.affymetrix] Error: object 'csC' not found.

Henrik Bengtsson-2
In reply to this post by ali jan
Still the same; you're not calling

csC <- process(acc, verbose=verbose)

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Re: [aroma.affymetrix] Error: object 'csC' not found.

321bixin
hello , i called the csC <- process(acc, verbose=verbose) and them print(csC), it still met Error: object 'csC' not found.
在 2017年11月24日星期五 UTC+8上午7:41:23,Henrik Bengtsson写道:
Still the same; you're not calling

csC <- process(acc, verbose=verbose)

--
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Re: [aroma.affymetrix] Error: object 'csC' not found.

Henrik Bengtsson-2
If you called

   csC <- process(acc, verbose=verbose)

and csC is not found, then there was an error during that call that you must pay attention to.

/Henrik

PS. Are you a single person reporting via three different email addresses, or are you two (three?) different people having the same problem?


On Friday, November 24, 2017 at 12:18:31 PM UTC-8, [hidden email] wrote:
hello , i called the csC <- process(acc, verbose=verbose) and them print(csC), it still met Error: object 'csC' not found.
在 2017年11月24日星期五 UTC+8上午7:41:23,Henrik Bengtsson写道:
Still the same; you're not calling

csC <- process(acc, verbose=verbose)

--
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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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