[BioC] GOStats question
Tarca, Adi
atarca at med.wayne.edu
Fri Apr 6 18:25:57 CEST 2007
Hi all,
I have a question about the output from GOstats.
What is the meaning Size column in the output of hyperGTest?
e.g.
GOBPID Pvalue OddsRatio ExpCount Count Size
GO:0046599 0 -17.44695071 0.103006873 2 1
GO:0043006 0 -17.50880134 0.309020619 6 3
....
I thought Size is the number of elements belonging to the GO term in the
specified universe, but it does not look to be so since the Count may be
higher than Size. Second question:
Is the hyperGTest returning the nominal Pvalues when used with a
GOHyperGParams instance, or they are somehow adjusted?
Thanks,
Adi L. Tarca
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