Dear Listers: I have a stat question on the senario like this: I have 6 genes and 2 biological pathways: gene 1-3 exclusively belongs to pathway A and gene 4-6 are shared by pathway A and B. If we observe gene 1-3 are differentially expressed, we have more confidence to say pathway A is activated in this situation than the one in which only gene 4-6 are observed to be differentially expressed. (In both situations, we do not know the expression levels for the rest genes). Scale up the situation to 1000 genes and 20 pathways for example, what kind of statistical approach should I use here to differentiate the situations above and is there a software in R or somewhere doing this? thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III