[BioC] GOHyperG

[Robert Gentleman]

On Feb 1, 2005, at 5:45 AM, Katleen De Preter wrote:

> Hello,
> I have some questions about GOHyperG:
> After performing GOHyperG test:
> > test1<-GOHyperG(listSAM1)
> I would like to obtain a table of GO-ids and description and p-value  
> of the first 10 GO-ids with lowest p-value.
> How can I do this?

The vignette is somewhat helpful in this regard, as is the manual page.
So, if you run the example,
  sort(xx$pvalues)[1:10]

seems like a start.

> Does someone know wheter GOHyperG corrects for multiple testing?

Umm, well the manual page is pretty explicit, I can only recommend that  
you read it.
There are no corrections made, you can make what ever ones you feel are  
appropriate, I personally know of no method that I would use or endorse  
for this situation.

  Robert


> Best regards,
> Katleen
>
>
>
> --  
> *dr. ir. Katleen De Preter*
> Center for Medical Genetics Ghent (CMGG)
> Ghent University Hospital
> Medical Research Building (MRB), 2nd floor, room 120.038
> De Pintelaan 185, B-9000 Ghent, Belgium
> +32 9 240 5533 (phone) | +32 9 240 6549 (fax)
> http://medgen.ugent.be
> Katleen.DePreter at UGent.be <mailto:Katleen.DePreter at UGent.be>
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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