Hi Sue, Your question doesn't make a lot of sense, because there have been no changes to the p-value columns output by topTable. The adj.P.Val column still exists as it always has, and there never has been a columun called "P". As pointed out by Jose, the problem is more likely to be that you are using the column tab$M which is now called tab$logFC. limma comes with lots of documentation. Why not just type ?topTable to see exactly what the columns are and what they mean? Alternatively, names(tab) would tell you the column names. Best wishes Gordon >Date: Thu, 30 Aug 2007 17:30:24 +0100 (BST) >From: Sue Jones <s.jones at="" sussex.ac.uk=""> >Subject: [BioC] topTable changes >To: bioconductor at stat.math.ethz.ch > >tab <- topTable(fit3, n=1500, adjust="fdr") > >The question I have is about the topTable function. Does this now only >produce a P.value column which contains the adjusted P-values and is this >column tagged as "P"? Are the two lines of code that extract the genes >with P values <0.05 correct? > >diff_exp <- tab2[tab2$P<0.05 & tab2$M<0.0,] >print("No down reg genes:"); length(diff_exp$ID) > > >previously I had code which used $adj.P.Val as a filter but this does not >work any more. > >Thanks > >Sue Jones >University of Sussex