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

[Chanchal Kumar]

Dear Jim,

   Thank you very much for the information. It was indeed very helpful.
Now I did my analysis with the "conditional" argument as TRUE and I see
that the result is more explainable. I am thinking of using this
conditional test in rest of my analysis. 

I will go through the reference as well.

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/
===============================


-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Monday, November 26, 2007 3:57 PM
To: Chanchal Kumar
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Query about the conditional hypergeometric test in
GOstats package

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
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