[BioC] Query about the conditional hypergeometric test in GOstats package

[James W. MacDonald]

Hi Chanchal,

The GO ontology is set up as a directed acyclic graph, where a parent 
term is comprised of all its child terms. If you do a standard 
hypergeometric, you might e.g., find 'positive regulation of kinase 
activity' to be significant.

If you then test 'positive regulation of catalytic activity', which is a 
parent term, then it might be significant as well, but only because of 
the terms coming from positive regulation of kinase activity.

The conditional hypergeometric takes this into account, and only uses 
those terms that were not already significant when testing a higher 
order (parent) term.

For a reference, see the paper by Adrian Alexa. You can find the 
citation on the last page of the 'How to use GOstats' vignette.

Best,

Jim


Chanchal Kumar wrote:
> Dear Bioconductor developers and users,
> 
>    I am using the "GOstats" package to find over/under enriched GO terms
> in my dataset. And there is an option to calculate the "conditional
> hypergeometric test". I am not sure what this would imply, I am aware of
> the conventional hypergeometric test but this is a bit unfamiliar
> concept. Therefore it will be very helpful if someone could explain the
> concept and point me to relevant references. 
> 
> Thanks in advance!
> 
> Best Regards,
> Chanchal 
> ===============================
> Chanchal Kumar, Ph.D. Candidate
> Dept. of Proteomics and Signal Transduction
> Max Planck Institute of Biochemistry
> Am Klopferspitz 18
> 82152 D-Martinsried (near Munich)
> Germany
> e-mail: chanchal at biochem.mpg.de
> Phone: (Office) +49 (0) 89 8578 2296
> Fax:(Office) +49 (0) 89 8578 2219
> http://www.biochem.mpg.de/mann/
> ===============================
> 
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-- 
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