[BioC] hyperGTest results I do not understand
ariel at df.uba.ar
ariel at df.uba.ar
Tue Feb 27 20:58:55 CET 2007
> 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
>
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