[BioC] gcrma with hgu133a and hgu133a2
MaximilianOtto at gmx.at
Wed Feb 27 23:30:59 CET 2008
I combined two affybatches (hgu113a and hgu133a2) with the matchprobes package. With the combined affybatch I could run rma. Now I would also like to run gcrma for which I would need a "hgu133aa2probe" package.
Can I make probe package from the new cdf file? Or could I simply subset the hgu133aprobe package with the probesets from the new cdf environment?
Thanks for your help!
Here's what I did:
comBatch <- combineAffyBatch(list(Data.a, Data.a2), c("hgu133aprobe", "hgu133a2probe"), newcdf = "hgu133aa2cdf")
comAffyBatch <- comBatch$dat
hgu133aa2cdf <- comBatch$cdf
eset <- gcrma(comBatch)
Adjusting for optical effect............................Done.
Computing affinities "Checking to see if your internet connection works..."
 "Environment hgu133aa2cdfcdf was not found in the Bioconductor repository."
 "Checking to see if your internet connection works..."
 "Environment hgu133aa2cdfprobe was not found in the Bioconductor repository."
Error in get(probepackagename) :
variable "hgu133aa2cdfprobe" was not found
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