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Hi, Please do not cross-post. Pick one list and post to it. Please spell and capitalize correctly: it is the affy package, not Affy, and perhaps the best answer to your question can be found at: http://affycomp.biostat.jhsph.edu/ and in particular "best" is not a well defined concept, it depends on what you want to achieve. best wishes Robert 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]] > > ______________________________________________ > R-help at 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. > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

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: roger.vallejo at ars.usda.gov > http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.