Roumyana Yordanova brought to my attention a mistake on the code suggestion I sent Peng on December 27th. The correct version is below (please note that normalization is performed on the original scale): library(oligo) data = read.celfiles(list.celfiles(data_dir, full=T)) idx = oligo:::getFidProbeset(data) theProbes = exprs(data[idx,]) bgData = rma.background.correct(theProbes) normData = log2(normalize.quantiles(bgData)) As a sanity check, I revisited oligo's code and everything there is as it should. Thanks a bunch, b On Dec 27, 2009, at 11:21 AM, Benilton Carvalho wrote: > library(oligo) > data = read.celfiles(list.celfiles(data_dir, full=T)) > idx = oligo:::getFidProbeset(data) > theProbes = exprs(data[idx,]) > bgData = rma.background.correct(theProbes) > normData = normalize.quantiles(log2(bgData)) > > On Dec 26, 2009, at 5:56 PM, Peng Yu wrote: > >> library(oligo) >> data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) >> pm(data) >> >> Do you mean the above commands? If that is the case, you misunderstood >> me. I don't need the original probe values. >> >> 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 <bcarvalh at="" 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 >>>> 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 >>> >>> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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