I am interested in using the function GOhyperG in the package GOStats but have the following challenge. I am using data from a u95av2 chip, but only about 25% of the genes are candidates for my analysis. Starting with these 3000 genes, I select those associated with my outcome of interest. To help with the interpretation of a relatively long list, I want to use function GOHyperG, as shown below. GOHyperG(GeneList, lib="hgu95av2", what="MF") I suspect I need to limit the GO terms I pass into the function to those associated with the 25% of genes that where the starting point of my analysis, not the full set for the 95av2 chip. I also suspect that this is not that hard for those who are well versed in manipulating the "affy chip packages." I have not been able to do this however. Is there an obvious easy solution that I am missing, or do I need to make an annotation package for my starting gene set from scratch? Neil Hayes ********************** Confidentiality Notice\ **********************\ The inf...{{dropped}}