[BioC] hyperGTest results I do not understand

[Seth Falcon]

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