Hi there, I've a question regarding to RMA in aroma: In a first step we've compared the normalization method used in aroma with the method used in the Affymetrix Powertools which gave us identical results. (500K chip) ("QuantileNormalization(cs)" vs "apt- cel-transformer") So in a next step we wanted to test median polish as well (standard flavor) on this data and compared it again to Affymetrix (using "apt- probeset-summarize" with med-polish,expr.genotype=true). We tried hard and tested a lot of configurations but we've never got the same results. (Same trend, but slightly different in the digits after the comma). R-script, quite straight forward: cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp"); cs <- AffymetrixCelSet$byName("testset", cdf=cdf); qn <- QuantileNormalization(cs); csN <- process(qn); plm <- RmaPlm(csN); fit(plm); The background correction was omitted in both scripts Any ideas? Thanks for your help Sebastian
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