The control names start with AFFX, so you can also: library(affy) mycels <-ReadAffy() myRMA <- rma(mycels) e = exprs(myRMA) controls <- grep("AFFX",rownames(e)) e <- e[-controls,] On Sat, Feb 18, 2012 at 5:05 AM, Yuan Hao <yuan.x.hao at="" gmail.com=""> wrote: > You can check out the genefilter package > > http://www.bioconductor.org/packages/release/bioc/html/genefilter.html > > Cheers, > Yuan > > > On 18 Feb 2012, at 09:33, Salwa Eid wrote: > >> >> >> >> >> Dear all, ? I read cel files from ncbi website using the readaffy(). ?Then >> i performed the expresso function to normalize using quantile normalization >> and retrieve rma expressions. ?Next I want to remove the affymetrix control >> probe sets from these expressions. ?Any help? Thanks,salwa >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor