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@ars.usda.gov http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 [[alternative HTML version deleted]]
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@ars.usda.gov http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 [[alternative HTML version deleted]]
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.
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: 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. >