Hi Seth, and thanks for your prompt response I do not think that this is a conditional analysis issue because the node I am focus on has no children. I did forget to take into account a specific ontology to make the contingency table. However I am still puzzled because even if I do filter on Ontology, the expected count value inferred from the new table does not agree with the one reported by GOstats either. New contingency table for BP: selected ~selected gonode 13 2 ~gonode 1230 1334 which gives ExpCount=7.229 (and not 13.8) So, if you do not mind, I accept your offer and I will send you, in private email, my selected and universe lists for you to check them. Thank you so much in advance Ariel./ I am running R 2.4 on Fedora 5 and here is the output of sessionInfo(): other attached packages: limma affy affyio Rgraphviz geneplotter xtable "2.9.1" "1.12.0" "1.2.0" "1.12.1" "1.12.0" "1.3-2" RColorBrewer GOstats Category KEGG RBGL GO "0.2-3" "2.0.0" "2.0.0" "1.14.0" "1.10.0" "1.14.0" graph genefilter survival annotate Biobase mouse4302 "1.12.0" "1.12.0" "2.29" "1.12.0" "1.12.0" "1.14.0" hgu133plus2 "1.14.0" Seth Falcon <sfalcon at="" fhcrc.org=""> ha escrito: > Hi Ariel, > > As always, it would help to know what versions you are using. Please > send the output of sessionInfo() (after running the example code). If > you aren't using the most current version of Category and GOstats, it > would be good to try updating. Read on for a few thoughts... > > ariel at df.uba.ar writes: >> I am learning how results reported by hyperGTest funcion are calculated >> but I am getting into trouble with some results I do not understand... >> In the following example 'selectedEntrezIds' is a list of 1507 >> non-duplicated >> modulated ENTREZ ids, included in 'entrezUniverse', a list of 3122 >> non-duplicated ENTREZ ids taken as the universe. >> >> Here is the code: >>> hgCutoff <- 0.05 >>> params <- new("GOHyperGParams", >> + geneIds=selectedEntrezIds, >> + universeGeneIds=entrezUniverse, >> + annotation="hgu133plus2", >> + ontology="BP", >> + pvalueCutoff=hgCutoff, >> + conditional=TRUE, >> + testDirection="over") > > 1. The input universeGeneIds are filtered to remove IDs that have no > annotation in the specified GO ontology. So if some of the 3122 > Entrez IDs you specified have no GO BP annotation, they will have > been removed from the universe. You can obtain the a list mapping > GO IDs to Entrez IDs using geneIdUniverse(hgOver.BP). So the > effective universe is unique(unlist(geneIdUniverse(hgOver.BP))). > > 2. You ran the hyperGTest with conditional=TRUE. See the vignette and > paper for details. You can obtain the conditional universe using > condGeneIdUniverse(hgOver.BP). > > If this extra info doesn't help, I'd be willing to take a closer look > if you can send the selected and universe lists (offline, of course). > > + seth >

> The fine print of my offer to look at your data was that you confirm > the issue with the latest versions ;-) yeah! You were right. I updated both, GOstats and Category and now I get the right expected number! Thanks Ariel./ Seth Falcon <sfalcon at="" fhcrc.org=""> ha escrito: > ariel at df.uba.ar writes: > >> Hi Seth, and thanks for your prompt response >> >> I do not think that this is a conditional analysis issue because >> the node I am focus on has no children. >> >> I did forget to take into account a specific ontology to make >> the contingency table. However I am still puzzled because even if I do >> filter on Ontology, the expected count value inferred from the new table >> does not agree with the one reported by GOstats either. >> >> New contingency table for BP: >> >> selected ~selected >> gonode 13 2 >> ~gonode 1230 1334 >> >> which gives ExpCount=7.229 (and not 13.8) >> >> >> So, if you do not mind, I accept your offer and I will send you, in >> private email, my selected and universe lists for you to check them. >> Thank you so much in advance > > There was a bug that may be related to this issue that has been > fixed. The current versions for use with R 2.4.x are GOstats 2.0.4 > and Category 2.0.3. > >> I am running R 2.4 on Fedora 5 and here is the output of sessionInfo(): >> >> other attached packages: >> RColorBrewer GOstats Category KEGG RBGL >> GO >> "0.2-3" "2.0.0" "2.0.0" "1.14.0" "1.10.0" >> "1.14.0" > > The fine print of my offer to look at your data was that you confirm > the issue with the latest versions ;-) > > Can you try getting the latest and giving this one more try. You > could update like this: > > source("http://bioconductor.org/biocLite.R") > biocLite(c("Category", "GOstats")) > > Or to get updates for all of your installed packages (may take awhile, > but is a good idea since updates usually mean bug fixes): > > library("Biobase") > update.packages(repos=biocReposList()) > > > Best, > > + seth >