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
>

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