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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 Aqu...

...rn("eset <- expresso(data, bgcorrect.method=" + Chr(34) + "rma" + Chr(34) + ", normalize.method=" + Chr(34) + "quantiles" + Chr(34) + ", pmcorrect.method=" + Chr(34) + "pmonly" + Chr(34) + ", summary.method=" + Chr(34) + "avgdiff" + Chr(34) + ")") 'Writng output data x.EvaluateNoReturn("write.exprs(eset,file=" + Chr(34) + "output.txt" + Chr(34) + ")") x.Close() ------ The "Close()" command should shutdown R and release all of the ownerships on files as R quits but...