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.
