I think I did not make myself clear. What I want to do is that after 
calling doASCRMAv2, I would like to extarct B allele freq data. Is this 
possible? I got error as following:

Error in UseMethod("extractTotalAndFracB") : 
  no applicable method for 'extractTotalAndFracB' applied to an object of 
class "c('AromaUnitTotalCnBinarySet', 'CopyNumberDataSet', 
'AromaUnitSignalBinarySet', 'AromaTabularBinarySet', 
'GenericTabularFileSet', 'GenericDataFileSet', 'FullNameInterface', 
Calls: extractTotalAndFreqB ... extractTotalAndFreqB.default -> 

My script looks like this:
celFiles <- AffymetrixCelSet$byName ('test', cdf=cdf)
ces<-doASCRMAv2 (celFiles, chipType="GenomeWideSNP_6,Full", verbose=-10)

theta <- extractTotalAndFreqB (ces[[1]])

There must be something wrong I did. 

Thanks for your time.


On Wednesday, March 18, 2015 at 10:42:06 AM UTC-4, Georg wrote:
> HI, there,
> I am a newbie to aroma.affymetrix. What I want to do is this, I want to 
> calculate the raw copy number and log2 ratio of a probe.
> I used doASCRMAv2 to normalize a single array's intensity values. Then 
> after that, I think I am supposed to use extractTotalAndFreqB to extract 
> total intensities and B-allele freq. The document I had missing one step, I 
> think, how to transform the output of doASCRMAv2 to the input of 
> extractTotalAndFreqB. So anyone can help how to do it? 
> BTW, I have searched internet for a good aroma.affymetrix tutorial, 
> however, without any good luck. If anyone can help to point to a direction, 
> it is very appreciated. Thanks.
> George

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