you might want to try it again avoiding the use of ReadAffy or read.affybatch. by never creating an AffyBatch and reading only a pm matrix you make a smaller object. as pointed out by james, this is what justRMA does. if you want RMA values and dont necesarily want to work within R/Bioconductor you might consider using: http://stat-www.berkeley.edu/users/bolstad/RMAExpress/RMAExpress.html On Tue, 10 Jun 2003, Puhong Gao wrote: > Rafael, > > Thank you very much for your input. I thought that, though quantile > nomalization only uses pm values by default, it will read in both pm and mm > values. > > I would love to test justRMA. But here is my dilemma. justRMA function is > available in R; but I have tried unsuccessfully to get the 150 cel files > into R. I managed to get the 150 cel files read into S-Plus ArrayAnalyzer > (no problem); but justRMA is not included in the ArrayAnalyzer. Any > suggestions? Is it possible to somehow port justRMA function to S-plus? > Thanks. > > Regards, > > Puhong > > ----- Original Message ----- > From: "Rafael A. Irizarry" <ririzarr@jhsph.edu> > To: "Puhong Gao" <pgao@hunter.cuny.edu> > Cc: <bioconductor@stat.math.ethz.ch> > Sent: Tuesday, June 10, 2003 1:45 PM > Subject: Re: [BioC] Affy Normalization! > > > > thats what quantile normalization does by default. to get the pms use the > > method: pm > > > > the function justRMA uses only pms and takes advantage of this to save on > > memory. you can look at the code for some hints. > > > > On Tue, 10 Jun 2003, Puhong > > Gao wrote: > > > > > Hi, all, > > > > > > To reduce the data size before quantile normalization, I am thinking to > > take PM intensity only (to solve memory problem). Is there a way to > > separate pm and mm data while the affybatch format is still perserved? If > > yes, is it appropriate to normalize the data based on the PM values only? > > Thanks in advance for your inputs. > > > > > > Data: from 150 u34a chips Computer: Windows XP pro with 2 GB of RAM > > > > > > Regards, > > > > > > Puhong Gao, PhD > > > Dev. Psychobiology > > > NYSPI, Unit# 40 > > > 1051 Riverside Dr. > > > New York, NY 10032 > > > (212) 543-5710 > > > [[alternate HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > >