HI,
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',
'Object')"
Calls: extractTotalAndFreqB ... extractTotalAndFreqB.default ->
extractTotalAndFracB
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.
George
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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