Hi, Is there a natural way to write normalized MA values along with the correct probe names? One can write the M and A values as tables but the row indices need not match the order of the probe names in the CEL files. Thank you for your help and my apologies if this is a trite question, Joel M. Malard, Ph.D. Scientist IV Pacific Northwest National Laboratory Battelle Boulevard, PO Box 999 Mail Stop K1-85 Richland, WA 99352 "I love the audacity of those who have everything to loose from it; the moderation of those who have nothing to gain from it." Rostand, Jean (1894-1977) [[alternative HTML version deleted]]

Hi Joel Depending on how you read your data in, the genes slot of your Rglist should be full of probe names. If it's not then you can set it by: RG$genes <- readGAL(...) Then, when you create and MAList from that RGList, the genes slot should be transferred over, so: out<-Cbind(MA$genes, MA$M) write.table(out,...) It's very important to realise that R and bioconductor, in many functions, relies on the fact that data in different files are in the same order - so if I read 12 gpr files in, it assumes they are ain Block,Row,Column order, and if they are not all in the same order, it doesn't do any cross-referencing. Hope that helps Mick -----Original Message----- From: Malard, Joel M [mailto:JM.Malard@pnl.gov] Sent: 12 October 2004 00:59 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Writing MAList to file (limma) Hi, Is there a natural way to write normalized MA values along with the correct probe names? One can write the M and A values as tables but the row indices need not match the order of the probe names in the CEL files. Thank you for your help and my apologies if this is a trite question, Joel M. Malard, Ph.D. Scientist IV Pacific Northwest National Laboratory Battelle Boulevard, PO Box 999 Mail Stop K1-85 Richland, WA 99352 "I love the audacity of those who have everything to loose from it; the moderation of those who have nothing to gain from it." Rostand, Jean (1894-1977) [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor