Dear List I want to do a hypergeometric testing of GO, KEGG and PFAM terms. I'm using the GOstats package and the method described in the vignette: "How to use GOstas and Category to do hypergeometric testing with unsupported model organisms" by M. Carlson, Oct. 31. 2011, because my organism is a non- model organisms. I have obtained the annotation for my gene sets from other sources and the method described in the vignette is working perfect for GO and KEGG. But now I would like to do the same for PFAM domains, but I'm having trouble figuring out how to do this. It seems that there is no function for creating a PFAMFrame object similar to the GOFrame and KEGGFrame functions, but I guess such an object could be constructed by other means, but I'm unsure how this is done? Many thanks for your time and help best, Henrik Licht [[alternative HTML version deleted]]

Hi Henrik, You are correct that there isn't a PFAMFrame yet. But the usage situation for PFAM should be very similar to what happens with KEGG. So theoretically, you should be able to use a KEGGFrame for this purpose. Have you tried this? Marc On 11/25/2011 02:12 AM, Henrik De Fine Licht wrote: > Dear List > > I want to do a hypergeometric testing of GO, KEGG and PFAM terms. I'm using > the GOstats package and the method described in the vignette: "How to use > GOstas and Category to do hypergeometric testing with unsupported model > organisms" by M. Carlson, Oct. 31. 2011, because my organism is a non-model > organisms. > > I have obtained the annotation for my gene sets from other sources and the > method described in the vignette is working perfect for GO and KEGG. But > now I would like to do the same for PFAM domains, but I'm having trouble > figuring out how to do this. > > It seems that there is no function for creating a PFAMFrame object similar > to the GOFrame and KEGGFrame functions, but I guess such an object could be > constructed by other means, but I'm unsure how this is done? > > Many thanks for your time and help > > best, > Henrik Licht > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor