[BioC] hyperGTest results I do not understand

[ariel at df.uba.ar]

> 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
>