[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
--



More information about the Bioconductor mailing list