[aroma.affymetrix] "Error: Failed to retrieve genome information" + paired samples

Gaius Augustus Fri, 13 May 2016 10:55:47 -0700

Hello,
I'm working on the Paired PSCBS protocol, and am running across an error.


Here is my file structure

-annotationData
---chipTypes
-----GenomeWideSNP_6
-------GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl
-------GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ugp
-------GenomeWideSNP_6,Full.cdf
-------GenomeWideSNP_6,HB20080710.acs
-------GenomeWideSNP_6.cdf
-rawData
---Samples
-----GenomeWideSNP_6
-------LIST OF CEL FILES



Everything seems to work fine in the Paired PSCBS protocol (except for one 
thing, which I'll ask at the end), until I run:

res <- doASCRMAv2(csR, verbose=verbose)

20160512 16:56:04|CRMAv2...
20160512 16:56:04| Arguments:
20160512 16:56:04| combineAlleles: FALSE
20160512 16:56:04| arrays:
  chr ""
20160512 16:56:04| Data set
 AffymetrixCelSet:
 Name: Samples
 Tags: 
 Path: rawData/Samples/GenomeWideSNP_6
 Platform: Affymetrix
 Chip type: GenomeWideSNP_6
 Number of arrays: 116
 Names: TCGA-3L-AA1B_Normal_Black, TCGA-3L-AA1B_Tumor_Black, TCGA-4N-
A93T_Normal_Black, ..., TCGA-WS-AB45_Tumor_Black [116]
 Time period: 2011-03-08 10:19:00 -- 2014-08-21 11:25:30
 Total file size: 7645.59MB
 RAM: 0.14MB
20160512 16:56:10| Checking whether final results are available or not...
20160512 16:56:10| Checking whether final results are available or not...
done
20160512 16:56:10| CRMAv2/Allelic crosstalk calibration...
[2016-05-12 16:56:11] Exception: Failed to retrieve genome information for 
this chip type: GenomeWideSNP_6


  at #28. getGenomeInformation.AffymetrixCdfFile(cdf)
          - getGenomeInformation.AffymetrixCdfFile() is in environment 
'aroma.affymetrix'


  at #27. getGenomeInformation(cdf)
          - getGenomeInformation() is in environment 'aroma.affymetrix'


  at #26. getSubsetToAvg.AllelicCrosstalkCalibration(this)
          - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment 
'aroma.affymetrix'


  at #25. getSubsetToAvg(this)
          - getSubsetToAvg() is in environment 'aroma.affymetrix'


  at #24. getParameters.AllelicCrosstalkCalibration(this, ...)
          - getParameters.AllelicCrosstalkCalibration() is in environment 
'aroma.affymetrix'


  at #23. getParameters(this, ...)
          - getParameters() is in environment 'aroma.core'


  at #22. getParameterSets.ParametersInterface(this, ..., drop = FALSE)
          - getParameterSets.ParametersInterface() is in environment 
'aroma.core'


  at #21. getParameterSets(this, ..., drop = FALSE)
          - getParameterSets() is in environment 'aroma.core'


  at #20. getParametersAsString.ParametersInterface(this)
          - getParametersAsString.ParametersInterface() is in environment 
'aroma.core'


  at #19. getParametersAsString(this)
          - getParametersAsString() is in environment 'aroma.core'


  at #18. sprintf("Algorithm parameters: %s", getParametersAsString(this))
          - sprintf() is in environment 'base'


  at #17. as.character.AromaTransform(x)
          - as.character.AromaTransform() is in environment 'aroma.core'


  at #16. as.character(x)
          - as.character() is local of the calling function


  at #15. print(as.character(x))
          - print() is in environment 'base'


  at #14. print.Object(...)
          - print.Object() is in environment 'R.oo'


  at #13. print(...)
          - print() is in environment 'base'


  at #12. eval(expr, envir, enclos)
          - eval() is local of the calling function


  at #11. eval(expr, pf)
          - eval() is in environment 'base'


  at #10. withVisible(eval(expr, pf))
          - withVisible() is in environment 'base'


  at #09. evalVis(expr)
          - evalVis() is local of the calling function


  at #08. capture.Verbose(this, print(...), level = level)
          - capture.Verbose() is in environment 'R.utils'


  at #07. capture(this, print(...), level = level)
          - capture() is in environment 'R.utils'


  at #06. print.Verbose(verbose, acc)
          - print.Verbose() is in environment 'R.utils'


  at #05. print(verbose, acc)
          - print() is in environment 'base'


  at #04. doCRMAv2.AffymetrixCelSet(..., combineAlleles = FALSE)
          - doCRMAv2.AffymetrixCelSet() is in environment 'aroma.affymetrix'


  at #03. doCRMAv2(..., combineAlleles = FALSE)
          - doCRMAv2() is in environment 'aroma.affymetrix'


  at #02. doASCRMAv2.default(csR, verbose = verbose)
          - doASCRMAv2.default() is in environment 'aroma.affymetrix'


  at #01. doASCRMAv2(csR, verbose = verbose)
          - doASCRMAv2() is in environment 'aroma.affymetrix'


Error: Failed to retrieve genome information for this chip type: 
GenomeWideSNP_6


*Problems*
1) As you can see, I'm getting the Failed to Retrieve genome information 
error.  Looking through the forums and the site, it seems that I only need 
the acs, ufl, cdf, and ugp files.  Those are in the annotationData folder. 
 So I assume I'm doing something else wrong.
2) I have ~60 paired samples I'd like to run through.  The example only 
notes how to do one set of paired samples.  Is there a simple way to denote 
many pairs?


Thanks,
Gaius

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[aroma.affymetrix] "Error: Failed to retrieve genome information" + paired samples

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