Hi,
so that example code uses the affy package of Bioconductor and not the
aroma.affymetrix framework. It might be that there is a bug in the
affy package or that it does not support custom CDFs well enough. It
could also be that the chip type you're using is special and not well
suited from customization.
I would recommend you to make sure your custom CDF first using the
doRMA() function in aroma.affymetrix.
/Henrik
PS. Please do not hijack old email threads; instead start with a new
message whenever you have a new topic.
On Fri, Dec 22, 2017 at 8:32 AM, Pabita Saud <pabita.bas...@gmail.com> wrote:
> Hi,
> I followed the aroma project to create a custom cdf package. I succeed in
> doing that. Now I want to see the expression of genes from a .cel file with
> my cdf package in compare to that with previous cdf. When I tried to use
> normalization (rma) to the affy object (with previous cdf), I can get
> expression set,
>
>>rawdata<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname ="syng007a520046cdf" )
>
>>rawdata
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=syng007a520046cdf (82661 affyids)
> number of samples=1
> number of genes=82661
> annotation=syng007a520046cdf
> notes=
>
>>rma(rawdata)
> Background correcting
> Normalizing
> Calculating Expression
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 82661 features, 1 samples
> element names: exprs
> protocolData
> sampleNames: GSM1090980_ZE010001.CEL
> varLabels: ScanDate
> varMetadata: labelDescription
> phenoData
> sampleNames: GSM1090980_ZE010001.CEL
> varLabels: sample
> varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: syng007a520046cdf
>
> But, if same process is applied to my cdf, I get an error,
>>rawdata_mycdf<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname
>> ="gpl16720syng007a520046.mycdf")
>>rawdata_mycdf
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=gpl16720syng007a520046.mycdf (8858 affyids)
> number of samples=1
> number of genes=8858
> annotation=gpl16720syng007a520046.mycdf
> notes=
>
>>rma(rawdata_mycdf)
> Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds
>
> I will really appreciate your help.
> Thank you.
>
> Best Regards,
> Pabita
>
> Best Regards,
> Pabita
[...]
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