[BioC] GOStats question

[James W. MacDonald]

Hi Adi,

Tarca, Adi wrote:
> 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:

You are correct. It looks like you have a relatively old devel version 
of GOstats, as Seth fixed that bug months ago. Try updating and see if 
you get correct values.


> Is the hyperGTest returning the nominal Pvalues when used with a
> GOHyperGParams instance, or they are somehow adjusted?

They are unadjusted p-values.

Best,

Jim


> Thanks,
> Adi L. Tarca
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.