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

Here is my file structure


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
 Name: Samples
 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...
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 

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

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

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

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

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

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

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

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

  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: 

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?


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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