On Thu, 17 Jun 2004, Simon Kidd wrote: > Do the p values that affylmgui uses to calculate the venn diagram > correspond to those given in the toptable lists? No, not exactly. (But I'm not an expert on this, so others may wish to correct me or clarify this further.) See the p.value argument in ?classifyTestsF and compare with the p.value in the object returned by eBayes (see ?eBayes). > If this is so we > should be able to get the same results by exporting the toptable > lists into Filemaker and doing various sorts there. Of course, you are welcome to export topTables and manually find genes which are above a certain cutoff in more than one topTable, but this will generally underestimate the number of genes in the intersection. classifyTestsF/vennCounts uses a more sophisticated method to count the genes in the intersection. Imagine a plot where you have a moderated t statistic for one contrast on a horizontal axis, and a moderated t statistic for another moderated t statistic on the other axis. If you want genes which are up-regulated in both contrats, you could just look for genes with t1 > 4 and t2 > 4, so the selected region on the t1,t2 plot would have a rectangular boundary. Whereas the classifyTestsF/vennCounts approach uses a curved boundary to decide which genes are up-regulated in both conditions. Thanks Anthony for the quick example of some venn diagram code in R, which was probably a response to my last post. But I was looking for something which actually used limma's classifyTestsF and vennCounts. The example in the help for ?vennCounts is: tstat <- matrix(rt(300,df=10),100,3) tstat[1:33,] <- tstat[1:33,]+2 clas <- classifyTestsF(tstat,df=10,p.value=0.05) a <- vennCounts(clas) So in your case, you need to get the tstat from affylmGUI. Let's say you have saved an .RData file from File-Save As in affylmGUI, called "affyDataContrastsComputed.lma" Now, load this file into a new R session: load("affyDataContrastsComputed.lma") Then extract the moderated t statistics of interest, after reading extract.pdf in the doc/ subdirectory of affylmGUI, in particular, please read the following lines: For example, the moderated t statistics can be obtained as follows: > ContrastParameterizationList[[1]]$eb$t tstat <- ContrastParameterizationList[[1]]$eb$t Then you can use the ?vennCounts example above. After you have computed your vennCounts object (called 'a' above), you can combine it with your probe set IDs as follows: geneIDs <- ls(getCdfInfo(RawAffyData)) where RawAffyData is an AffyBatch object. class(a) <- "matrix" data.frame(geneIDs=geneIDs,a) This should give you the list of genes in the intersection. Apologies for using the old limma style of storing the empirical bayes statistics in a separate object "eb" rather than "fit", but generally this sort of thing is updated much more gradually in the GUI compared with limma. Hope this helps, James ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au