You can get more specific answers if you ask more specific questions.
mathematical formulation of the test(s), and therefore the meaning of
results, will depend directly on
1) the logic of the package you use to test for GO enrichment in a
2) the logic of the package you use to test for KEGG enrichment in a
list or lists
A concise and useful description of the logical basis for
You mention GSEA simultaneously with GO/KEGG enrichment, thus perhaps
would be best if you provide examples making your question more
that others may benefit. For example, the logic behind the similarly-
GSA and GSEA procedures differs subtly. On that note, you might find
following two discussions helpful:
If you haven't already, you will want to read the original GSEA paper
PNAS for background.
On Thu, May 5, 2011 at 8:20 AM, Radhouane Aniba <email@example.com>
> 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
> GOstats, GSEA etc ..
> My question is : I am working with 4 differents genomes, I have gene
> for each of them, and I want for a given gene for each list for each
> - Extract the GO with its pvalue (what does the pvalue actually mean
> enrichment ok but how is it calculated ? )
> - Extract the KEGG pathway and its pvalue as well
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> Bioconductor mailing list
> Search the archives:
If people do not believe that mathematics is simple, it is only
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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