1. This question is more appropriate for the BioConductor mailing list. 2. Any Affymetrix pre-processing can be split into background correction, normalisation and summary stages. The combination of rma background, quantile normalisation and median polish summary gives rise to RMA. Therefore quantile normalisation is a defining feature of RMA. ( which is probably why when the authors of RMA improved the background stage, they called it GC-RMA instead ).
3. You can certainly mix and match any stages you like using the expresso function. See help(expresso). On Thu, 2004-10-21 at 21:14, Hairong Wei wrote: > Can anybody explain why RMA has to have a default normalization method: > quantile-quantile? Why don't leave the choices to users? > > If I just want to use RMA to do a background correction without > normalization, how should I specify the ? in the normalize.method="?" ? > > > > Hairong > > > [[alternative HTML version deleted]] > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > ______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
