Hello, Can anybody advise me on how to get gene-level rma vs. probe-level rma using rma(...) method in the Affy package for the HTHGU133A platform? Thank You, Aaron [[alternative HTML version deleted]]

Hi AaronYou can try this code below. Much of this has been compiled from information out of R vignettes and the RMA Express website (*rma* express.bmbolstad.com). Before doing all this you may want to either download and/or install the correct libraries to read in your chips. After you have done that: For standard RMA normalization i.e. gene-level data > library(affy) > setwd("<your working="" dir="" that="" has="" the="" cel="" files="">") > eset<-justRMA() You can also do > data<-ReadAffy() > eset<-rma(data) To write out your data > write.exprs(eset,file="eset.txt") Get probe level unnormalized intensities of Affy data > pmdata=log2(pm(data)) # for 2-logged data > write.table(pmdata,file="my_pm_data.txt",sep="\t") > data2=exprs(data) # for unlogged data > write.table(data2,file="my_data.txt",sep="\t") If you need probe-level intensities (unnormalized) w. corresponding probe names rather than the probe index numbers as above will provide: > y=pm(data,geneNames(data)) # for unlogged data > write.table(y,file="file.txt") > y2=log2(pm(data,geneNames(data))) # for 2-logged data > write.table(y2,file="file2.txt") If you need normalized but unsummarized probe level intensities i.e. individual probes' intensities after background correction > data = ReadAffy() > my.PM <- apply(pm(data), 2, bg.adjust) > my.Quan <- normalize.quantilesmy.PM) > y2=log2(pm(data,geneNames(data))) > Quan_log<-log2(my.Quan) > rownames(Quan_log)=rownames(y2) > colnames(Quan_log)=sampleNames(data) > write.table(Quan_log,"rma_abatch_norm.txt") > write.table(Quan_log,"rma_abatch_norm.txt",quote=F,sep="\t") On Mon, Jan 12, 2009 at 10:17 AM, Skewes,Aaron <askewes@mdanderson.org>wrote: > Hello, > > Can anybody advise me on how to get gene-level rma vs. probe-level rma > using rma(...) method in the Affy package for the HTHGU133A platform? > > Thank You, > Aaron > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Aaron, Can you clarify this a bit? By probe-level rma do you mean probeset-level? What do you mean by gene-level? Best, Jim Skewes,Aaron wrote: > Hello, > > Can anybody advise me on how to get gene-level rma vs. probe-level rma using rma(...) method in the Affy package for the HTHGU133A platform? > > Thank You, > Aaron > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662