Damn, this was a cross-post (and I replied to all), apologies for my re-cross-posting.
To Roger, the original poster: PLEASE do read the posting guide of R-help before posting and NEVER EVER do crossposting again. Thanks, Uwe Ligges Uwe Ligges wrote: > > > Vallejo, Roger wrote: >> Dear R Users, >> In the expresso function, which combination of these methods for data >> pre-processing (when using affymetrix oligo arrays) is the best: >> >> bgcorrect.metod = rma rma2 mas >> >> normalize.method = qspline quantiles loess >> >> pmcorrect.method = pmonly subtractmm mas >> >> summary.method = liwong avgdiff medianpolish mas >> >> There are many options within each method. I would appreciate a hint >> on the best combination. > > > There is more than one implemented, hence we can guess that there is no > generally best one among these, i.e. it depends on your data what to use. > > Uwe Ligges > > >> Thank you very much in advance. >> Roger >> >> >> Roger L. Vallejo, Ph.D. >> Computational Biologist & Geneticist >> U.S. Department of Agriculture, ARS >> National Center for Cool & Cold Water Aquaculture >> 11861 Leetown Road >> Kearneysville, WV 25430 >> Voice: (304) 724-8340 Ext. 2141 >> Email: [EMAIL PROTECTED] >> http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.