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 --

Hi Max, Max Kauer wrote: > 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? You will need another package called hgu133aa2probe. You also want to call your newcdf 'hgu133aa2' without the cdf at the end. Note the error where R can't find hgu133aa2cdfcdf below. You might be able to simply take the hgu133a2probe package and rename and install as hgu133aa2. But then maybe not -- I have never tried it, and I don't know offhand what all you will need to rename. Certainly the package itself, and parts of the DESCRIPTION file. An alternative is to get the hgu133a2_probe_tab file from affy and subset it to only contain the probesets that are in your new cdf. Then build the probe package using makeProbePackage() in matchprobes. Either way, you will need to be able to install the package, so if you are on Windows you will also need to get set up to install packages. See the R Windows FAQ, specifically 7.1. Best, Jim > > 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 > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623