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Hi Ng, include='both' will mark a gene as differentially expressed or not differentially expressed, ignoring the direction. If your categories are A, B and C, a gene that is up in A & B and down in C will end up at the intersection of the three categories include=c('up','down') will do two comparisons. The first ('up') marks the gene as overexpressed or not (i.e. underexpressed or unchanged). The second does the opposite and only counts underexpressed genes. You will notice that both sets of counts include the total of your genes, as they cannot be considered together. The previous example that is up in A & B and down in C would end up being in the A&B intersection in 'up', and in C only in the 'down'. Please tell me if this is not clear. I am unsure which labels you are talking about that you would like to move to the left hand side. Unfortunately, the positions for labels are hard-coded in this function. One way would be to use fix(vennDiagram) to change them if you want. If you tell me which ones you want exactly, I could send you another version with the position changed. Francois Ng Stanley wrote: > Hi, > > Two questions: > A) I don't understand the difference between include=c("up", "down"), and > include="both". The numbers for both venn diagram are different. > B) How to label on the left hand side ? > > Thanks > Stanley > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor