Hi Roger, If you do not use a standard set of methods (e.g. rma or gcrma) then you will need to justify your choice to your publication audience. So, I do not use these primary methods unless I have a compelling reason to do so. --Naomi At 05:55 PM 12/26/2007, 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. >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: roger.vallejo at ars.usda.gov >http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111