Hello all, I am working with data with a very large number of differentially expressed genes (liver cancer samples), and wish to demonstrate for my advisor and committee the effect of choosing different pre-processing methods. To do this, I have normalized the data in several different ways and genereated DEG lists with limma and decideTests. Now I would like to examine the difference in which probesets are called by the various methods. I've read everything I can find about the venn tools in limma and vennSelect, but they only seem to compare the output of different contrasts within a single dataset. Can someone suggest how to compare the output of the same contrast in a dataset processed 2 ways? I could output to Microsoft Access, but surely there is a better way!! Thanks so much, Mikki Behnke Integrative Life Sciences Virginia Commonwealth University [[alternative HTML version deleted]]