Hi Diana, the 'issue' you are seeing is due to the "True Path Rule". I suspect that the geneID2GO mappings gives only the specific annotation to a particular GO term. However during the mapping of the genes to the GO hierarchy the genes annotated to a GO term are pushed up the hierarchy. So a GO term will contain the genes specifically annotated to it plus all the genes present in the children (and it goes recursively). The root of the hierarchy will contain all the genes in the gene universe. This is why the numbers you see larger numbers in GenTable. Also if you want to run an enrichment test on the GO term containing only the specific annotated genes, you don't need to use topGO (it is a case of applying a hypergeometric test to each group), but that is usually not the case or desired. Hope this clarifies your issue. Best regards, Adrian [[alternative HTML version deleted]]

Thanks, Adrian- That is most likely what is going on. It's not something I've encountered in the past, but really good to know. Thanks again! -Diana On Mon, Sep 2, 2013 at 8:42 AM, Adrian Alexa <adrian.alexa@gmail.com> wrote: > Hi Diana, > > the 'issue' you are seeing is due to the "True Path Rule". I suspect that > the geneID2GO mappings gives only the specific annotation to a particular > GO term. However during the mapping of the genes to the GO hierarchy the > genes annotated to a GO term are pushed up the hierarchy. So a GO term will > contain the genes specifically annotated to it plus all the genes present > in the children (and it goes recursively). The root of the hierarchy will > contain all the genes in the gene universe. > > This is why the numbers you see larger numbers in GenTable. Also if you > want to run an enrichment test on the GO term containing only the specific > annotated genes, you don't need to use topGO (it is a case of applying a > hypergeometric test to each group), but that is usually not the case or > desired. > > Hope this clarifies your issue. > > > Best regards, > Adrian > [[alternative HTML version deleted]]