I have changed the subject line to something more appropriate. In R 2.5.1 and Bioconductor 2.0, the recommended way to do what you want (select DE genes on the basis of a combination of p-value and log fold change) was to use decideTests(). In R 2.6.0 and Bioconductor 2.1, you will find that topTable() now has p-value and logFC arguments which allow you to do the same thing using topTable(). Best wishes Gordon >Date: Wed, 3 Oct 2007 17:31:34 +0100 (BST) >From: Lev Soinov <lev_embl1 at="" yahoo.co.uk=""> >Subject: Re: [BioC] design matrix >To: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> >Cc: bioconductor at stat.math.ethz.ch >Message-ID: <412385.24484.qm at web27908.mail.ukl.yahoo.com> >Content-Type: text/plain > >Dear List, > > Could you help me with another small issue? > I usually write out the results of my analysis using the > write.table function as follows: > > Assuming 30000 probes in the dataset: > data <- ReadAffy() > eset <- rma(data) > > design <- model.matrix(~ -1+factor(c(1,1,1,2,2,3,3,3))) > colnames(design) <- c("group1", "group2", "group3") > contrast.matrix <- makeContrasts(group2-group1, group3-group2, > group3-group1, levels=design) > > fit <- lmFit(temp, design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) > > C1<-topTable(fit2, coef=1, number=30000, adjust="BH") > >write.table(C1,file="comparison1.txt",append=TRUE,quote=FALSE,sep="\t ",row.names=TRUE,col.names=FALSE) > > C2<-topTable(fit2, coef=2, number=30000, adjust="BH") > >write.table(C2,file="comparison2.txt",append=TRUE,quote=FALSE,sep="\t ",row.names=TRUE,col.names=FALSE) > > C3<-topTable(fit2, coef=3, number=30000, adjust="BH") > >write.table(C3,file="comparison3.txt",append=TRUE,quote=FALSE,sep="\t ",row.names=TRUE,col.names=FALSE) > > I then use the written out txt files (comparison1.txt, > comparison2.txt and comparison3.txt) to select significant probes > on the basis of log2fold change and adjusted p values thresholds, using Excel. > Would you say that this is a correct way to do this and could you > please recommend me some other, may be more efficient way of > writing the results of topTable for all 30000 probes out? > > With kind regards, > Lev.