Hello I thought I would ask the list before writing something myself. Commonly with microarray data, you end up with a list of genes that are UP, and a list of genes that are DOWN. We then put these lists through some sort of enrichment process to see which GO terms are enriched in each list. My current problem is that the enriched GO terms are similar: for example, in my list of UP genes, the top 3 CC GO terms are Cytoplasm, Nucleus, Membrane. In my list of DOWN genes, the top 3 CC GO terms are... Cytoplasm, Nucleus, Membrane! So the question is how to find the differences! Now, before I start hacking away with intersect(), union(), setdiff(), merge() etc, has anyone else written something already? Thanks Mick [[alternative HTML version deleted]]