Jason, This is another point I have been trying to understand. In some experiments I have had B values of over 22 and others only 6. Are these values directly comparable or do they suggest that in a set where the numbers are low (say 6 and below) that most of the genes are unlikely to be differentially expressed? Any thoughts welcome. I think this hits the point that looking at lists shouldn't be solely about the numbers of genes you want to look at. If you see low values should you look at look at a smaller top hits list (30 genes vs 50) and in a different experiment where you have higher values you should look at more (top 100 vs top 50). Any thoughts? Liz Molteno Building Department of Pathology University of Cambridge Tennis Court Road Cambridge, CB2 1QP United Kingdom Website: http://www.path.cam.ac.uk/~toxo/ Tel 01223 33 33 31(office) or 01223 33 33 29 (lab) ----------------------------------------- Message: 20 Date: Thu, 19 Aug 2004 12:40:57 -0400 From: "Jason Hipp" <jhipp@wfubmc.edu> Subject: RE: [BioC] B statistic in limmaGUI Cc: <bioconductor@stat.math.ethz.ch> Message-ID: <1D7037B603266D4082E413CDB2FE857A08164FC5@EXCHVS1.medctr.ad.wfubmc.edu > Content-Type: text/plain; charset="iso-8859-1" What is the difference between a B value of 1 vs 2 vs 10? How high can a B value go? Thanks, Jason