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

[Chanchal Kumar]

Dear Dr. Gentleman,

  Thanks for the inputs. It was indeed helpful and now after reading the
references the concept is pretty clear.

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: Robert Gentleman [mailto:rgentlem at fhcrc.org] 
Sent: Monday, November 26, 2007 5:36 PM
To: James W. MacDonald
Cc: Chanchal Kumar; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Query about the conditional hypergeometric test in
GOstats package

a bit more info
   1) there are two packages GOstats (Falcon and Gentleman) and topGO 
(Alexa), that do conditional analyses are very similar in spirit. They 
were developed independently, but at about the same time

  2) and each has its own reference,
   ours is
      S. Falcon and R. Gentleman, Using GOstats to test gene lists for 
GO term association,
Bioinformatics, 2007, 23, 257-258.

   Jim already provided the other one


   and the vignette for the package should also provide some reasonable 
explanation and examples,

   best wishes
     Robert


James W. MacDonald wrote:
> 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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> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org