[BioC] Odds Ratio in GOstat

Naomi Altman naomi at stat.psu.edu
Mon Dec 11 22:51:53 CET 2006

One thing I noticed is that the "universe" sent by the investigator 
does not include all the genes in the test set.  However, using the 
union of the 2 sets as the universe does not fix the problem.


At 03:02 PM 12/11/2006, Seth Falcon wrote:
>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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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