[BioC] hyperGTest results I do not understand

[ariel at df.uba.ar]

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
>