Thank you.
Best Regards,
Pabita
On Fri, Dec 22, 2017 at 12:02 PM, Henrik Bengtsson <
henrik.bengts...@gmail.com> wrote:
> 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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