Christine, On Tue, 23 Sep 2003 c.chaffer@pgrad.unimelb.edu.au wrote: > Hi James, > > How's it going? I have a question for you!! > > I've been playing with my data in Limma and am wondering if there is a way > to get a list of the genes that are represented in the intersection of the > venn diagram?? Use classifyTests to get a classification object "clas" which you can use in vennCounts. Then you can use : clasWithGenes <- cbind(genelist,clas$classification) to combine the genelist information with the classification. Make sure that nrow(genelist)==nrow(clas$classification). If not, you might need to run unwrapdups on genelist. Then to see only the rows of clasWithGenes with genes upregulated in both comparisons, use : clasWithGenes[clasWithGenes[,"Control-Ref"]==1&clasWithGenes[,"KO- Control"]==1,] The number of rows of this result should be the same as the corresponding count in vennCounts(clas,include="up") Regards, James