I think that you misunderstood me. As far as I know, RMA does three things: background correction, quantile normalization, and summary from probes to probesets. I want the probe values after background correction and quantile normalization but before the summary.
On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarv...@jhsph.edu> wrote: > pm(data) > > b > > On Dec 26, 2009, at 2:21 PM, Peng Yu wrote: > >> I use the following code to do RMA. I'm wondering how get the probe >> level values before the summary to the probeset level values. >> >> library(oligo) >> data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) >> eset<-rma(data) >> write.exprs(eset, file='output_file_name', sep="\t") >> >> _______________________________________________ >> Bioconductor mailing list >> bioconduc...@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
