[BioC] Odds Ratio in GOstat

Seth Falcon sfalcon at fhcrc.org
Mon Dec 11 21:02:57 CET 2006

Hi Naomi,

Naomi Altman <naomi at stat.psu.edu> writes:
> I am getting some rather odd "OddsRatio" numbers in my GOstat 
> tables.  In particular, I seem to be getting "Inf" whenever 
> "Observed"="Size".  This does not seem to be right, unless "Size" is 
> the number of hits in the union of the test and nontest set.  But if 
> that is the case, then "Size" should always be greater than or equal 
> to "Observed" and that is not the case.

Hmm, I will certainly look into this.  Can you provide some
sessionInfo() information?

The "Size" column is the number of genes annotated at the given GO
term (where genes are restricted to the defined gene universe).  You
are right that Size should always be greater or equal to the observed
count.  Jim found a bug relating to this which I fixed.  If you don't
already have Category 2.0.3 and GOstats 2.0.4, could you try upgrading
(via biocLite) and let me know if you still see the problem?

+ seth

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