I have a class of spots on my arrays called "blank" that I would like to remove from topTable output. I didn't see an easy way to do this in any of the options. --Dennis

Dear Dennis, I has the some problem yasterday and I fix it with a sub set. I group this blank in the end of the data file. For example, from 1 to 2576 genes I have the "true" data. From 2577 to 2898 I have the blank genes. When I execute the limma commands, I sub set it. MA<-normalizeWithinArrays(RG, layout) MA<-normalizeBetweenArrays(MA,method="scale") cor<-dupcor.series(MA$M[1:2576,],design,ndups=2,spacing=4) fit<-lmFit(MA[1:2576,],design,ndups=2,spacing=4,correlation=cor$cor) eb<-eBayes(fit) TopTableresult<-topTable(eb,number=100,adjust="fdr") write.table(TopTableresult,"result.txt",sep="\t") I dont known if this is the best way for this, but, for me, it solve my problem, I think. My excuses if it is wrong. Hope this help Marcelo Em Fri, 07 May 2004 10:46:49 -0700 Dennis Hazelett <hazelett@uoneuro.uoregon.edu> escreveu: DH> I have a class of spots on my arrays called "blank" that I would like to DH> remove from topTable output. I didn't see an easy way to do this in any DH> of the options. DH> DH> --Dennis