Hi Radhouane,

You can get more specific answers if you ask more specific questions.  The
mathematical formulation of the test(s), and therefore the meaning of your
results, will depend directly on

1) the logic of the package you use to test for GO enrichment in a gene list
or lists
2) the logic of the package you use to test for KEGG enrichment in a gene
list or lists

A concise and useful description of the logical basis for hypergeometric and
binomial tests:

http://great.stanford.edu/help/index.php/Statistics#What_is_the_hypergeometric_test_formally.3F

You mention GSEA simultaneously with GO/KEGG enrichment, thus perhaps it
would be best if you provide examples making your question more concrete, so
that others may benefit.  For example, the logic behind the similarly-named
GSA and GSEA procedures differs subtly.  On that note, you might find the
following two discussions helpful:

http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ#What_is_the_difference_between_GSEA_and_an_overlap_statistic_.28hypergeometric.29_analysis_tool.3F

http://www-stat.stanford.edu/~tibs/ftp/GSA.pdf

If you haven't already, you will want to read the original GSEA paper in
PNAS for background.

Best regards,

--t


On Thu, May 5, 2011 at 8:20 AM, Radhouane Aniba <aradwen@gmail.com> wrote:

> Hello everyone,
>
> Well I am aware of some packages in Bioconductor that are useful for
> measuring the GO or KEGG gene enrichment in a given file for a given
> genome,
> GOstats, GSEA etc ..
>
> My question is : I am working with 4 differents genomes, I have gene lists
> for each of them, and I want for a given gene for each list for each
> geneome
> :
>
> - Extract the GO with its pvalue (what does the pvalue actually mean here,
> enrichment ok but how is it calculated ? )
> - Extract the KEGG pathway and its pvalue as well
>
> Thanks
>
> Rad
>
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>
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-- 
If people do not believe that mathematics is simple, it is only because they
do not realize how complicated life is.
John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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