Something like "rma(data, background = MAS, normalize = FALSE)" will work for you. Actually, there are a lot of options for users to choose. good luck. Frank Quoting Fangxin Hong <fhong@salk.edu>: > There are some alternatives to do background correction and normalization > separately, and you can specify he methods you want to us. > > like > data.bg<-bg.correct.mas(data) > data.bg.nor<-normalize.AffyBatch.quantilesdata.bg, type="together") > > Fx > > > Can anybody explain why RMA has a default normalization method: > > quantile-quantile? Why don't leave the choices to users? > > > > > > > > If I just want to run RMA for a background correction without > > normalization, > > how should I specify the in the expresso function, in > > the other word, normalize.method="?" > > > > > > > > Hairong > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > -- > Fangxin Hong, Ph.D. > Plant Biology Laboratory > The Salk Institute > 10010 N. Torrey Pines Rd. > La Jolla, CA 92037 > E-mail: fhong@salk.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >