Greetings all, Using limma's fitting approach and topTable(), I have reached the nice point of having produced lists of annotated interesting genes. Graphically, I can now compare across my contrasts using Venn diagrams, and I can build Volcano plots etc. As I am making my early steps into Gene Ontology, I believe that the audience before which I will present my data will expect me to highlight which Biological Processes were significantly (and with what significance) involved in my experiments, and what differences I found across my contrasts. What solutions are available via Bioconductor to address these data analysis and reporting questions? Is GOstats useful in this regard? My major reference is ' Bioinformatics and computational biology solutions using R and Bioconductor'. I have tried to use the annaffy package and aafTableAnn(), with its subsequent html export mode, but this outputs all three ontologies, whereas I may wish to limit myself to Biological Processes for the moment. Also, I would prefer to see an output in which BP GOs are listed with the number of my 'interesting genes' falling into them. Not sure whether this is a standard way of reporting these data, but I hope that you may have some simple advice on this matter. Thanking you in advance, Yours, Massimo P. Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto