[BioC] gcrma with hgu133a and hgu133a2
Max Kauer
MaximilianOtto at gmx.at
Wed Feb 27 23:30:59 CET 2008
Hi
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!
Max
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[1] "Checking to see if your internet connection works..."
[1] "Environment hgu133aa2cdfcdf was not found in the Bioconductor repository."
[1] "Checking to see if your internet connection works..."
[1] "Environment hgu133aa2cdfprobe was not found in the Bioconductor repository."
Error in get(probepackagename) :
variable "hgu133aa2cdfprobe" was not found
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