[BioC] GO enrichment for genome-wide analysis

[James W. MacDonald]

burak kutlu wrote:
> Hi, My understanding is that GOstats implements the GO term
> enrichment analysis for studies using microarrays (where the lib
> argument is passed to "GOHyperG" to define the microarray-specific
> environment, therefore the gene universe). I was wondering if there
> is a readilly-available function for determining GO term significance
> that uses the GO terms from the whole genome rather than the GO terms
> from the genes represented on an array. 

I don't think you will find this anywhere, because it doesn't make 
sense. The idea behind GOHyperG is similar to the canonical 'ball and 
urn' scenario used in basic stats to explain the Hypergeometric 
distribution.

The goal is to determine the probability of reaching into an urn 
containing a certain number of black and white balls, removing x balls 
and having n of those balls be white.

Your question is akin to asking the probability of reaching into an urn 
containing black and white balls, removing x balls and having n of those 
balls be white, but based on the relative proportion of black and white 
balls in the world, instead of the proportion of black and white balls 
in the urn. Since the proportion of black and white balls may be quite 
different in the urn as compared to the world, you cannot generalize 
like that.

Best,

Jim


Please point me to this
> function if I have failed to find it in the documentation. Thanks 
> -Burak Kutlu
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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