Hi Seth, Thanks for your replay I actually had duplicates in my gene universe. Running hyperGTest now (without duplicates) gives meaningful results. all the best, Ivan Quoting Seth Falcon <sfalcon at="" fhcrc.org="">: > Hi Ivan, > > ivan.borozan at utoronto.ca writes: >> I got following results using hyperGTest(params) with a given list of genes >> >>> summary(hgOver) >> GOBPID Pvalue OddsRatio ExpCount Count Size >> 1 GO:0030185 0.000000e+00 -73.314685 0.02692165 2 1 >> 2 GO:0006067 0.000000e+00 -110.746479 0.05384330 3 2 >> 3 GO:0006069 0.000000e+00 -110.746479 0.05384330 3 2 > > Hmm, that is a suspect result. One would expect Size >= Count. In > the current devel version of Category and GOstats, I have added code > to verify that the selected gene list (geneIds) and the gene universe > do not contain any duplicates. Could you verify that your input does > not contain duplicate IDs either in the selected list or the universe? > >> If for example I look at genes that are associated with the first GO >> term (i.e GO:0030185) I get: >> >> >>> probeSetSummary(hgOver)[[1]] >> EntrezID ProbeSetID selected >> 1 3043 144221 0 >> 2 3043 148425 0 >> 3 3043 3108408 0 >> 4 3043 5708746 0 > > This is, of course, also surprising, but it is difficult to assess > what is going on without knowing more details of what data you used as > input. Are you sure that all Entrez IDs in geneIds(params) are > represented by at least one probe set on the chip? > >> My question is how are Counts (in this case Count = 2) in the above >> summary(hgOver) table obtained ? > > The details are in the code, but the intention is that Count is the > intersection of the selected gene list with the Entrez IDs annotated > at the given GO term. > >> Looking at probeSetSummary(hgOver)[[1]] I can see one EntrezID >> (EntrezID = 3043) and 4 ProbeSetID associated with this particular >> node (i.e GO:0030185). > > That just tells you that there are 4 probesets that interrogate Entrez > ID 3043. The count in the hyperGTest result tells you that 2 Entrez > IDs from the selected gene list are in the list of genes annotated at > GO:0030185. > > I have added a considerable amount of detail to the GOstats vignette > in the current devel repository and I would suggest reading over it: > > http://www.bioconductor.org/packages/1.9/bioc/html/GOstats.html > > + seth >