[BioC] hypergeometric test in GOstats

Sebastien Gerega seb at gerega.net
Thu Mar 12 02:47:35 CET 2009

I would like to get a better understanding of exactly how the 
calculations in GOstats are performed.
Does the package use a standard hypergeometric test?
If I have the following values:
geneIds = 266
universeGeneIds = 1803

and a particular GO term has:
size = 124
count = 55

then the associated p-value, odds ratio and expected count are 
1.519928e-16, 5.660429, and 18.81197 respectively.

However, I would have thought the expected count would be 266 * 124 / 
1803 = 18.29. In addition, the p-value obtained from the hypergeometric 
test using the following website http://keisan.casio.com/has10/SpecExec.cgi
is different.

Are there any steps performed by the GOstats package that make it 
different from a standard hypergeo test? What is the reason for these 
thanks in advance,

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