[BioC] which universe in hyperGTest

[James W. MacDonald]

Seth Falcon wrote:
> "James W. MacDonald" <jmacdon at med.umich.edu> writes:
> 
>>You can test for under-represented GO terms by setting the testDirection 
>>argument of your GOHyperGParams object to "under". So if your 
>>GOHyperGParams object were set up like this:
>>
>>params <- new("GOHyperGParams", geneIds = A, geneUniverseIds = ALL)
>>
>>then you would test for over representation as normal:
>>
>>hyperGTest(p)
>>
>>and under-representation like this:
>>
>>testDirection(params) <- "under"
> 
> 
> make that: testDirection(p) <- "under"
> 
> and then:
> 
> 
>>hyperGTest(p)
> 
> 
> 
> I knew what you meant, but in case someone thinks "params" is a magic
> word...

This just goes to show the power of the vignette. I usually call my 
GOHyperGParams objects 'params', but reverted to what you call it in 
your vignette, right in the middle of my example. Now if I could just 
get my computer to be able to figure out what I mean when I mix things 
up like that. ;-D

Best,

Jim


> 
> :-)
> 
> + seth
> 
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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


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