[BioC] hypergeometric enrichment of GO terms

[Thomas Girke]

Axel,
Here is a R/BioC script that performs the phyper test on your own data sets:
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#GOHyperGAll

The last function "simplifyDF" (4.2) is an attempt to address the problem with nested
categories. As pointed out by Wolfgang there doesn't appear to be an efficient 
solution to this problem.

Thomas

On Mon 08/21/06 17:39, Wolfgang Huber wrote:
> Hi again,
> 
> I should have added that the example mentioned below does not tackle the 
> problem of selecting the 'most meaningful' category out of a set of 
> nested categories that are all enriched. That is hard problem and I am 
> not sure it has an objective solution. I have been doing it manually, 
> and for doing that recommend looking at a plot showing the GO graph 
> together with the enrichment p-values [like, for example, in Fig. 4 of 
> the vignette of the GOstats package "Using GO for Statistical Analyses".]
> 
>    Best wishes
> 	 Wolfgang
> 
> 
> Wolfgang Huber wrote:
> > Chapter 8 of the vignette of the cellHTS package
> > http://www.bioconductor.org/packages/1.9/bioc/vignettes/cellHTS/inst/doc/cellhts.pdf 
> > gives an example on how to do this on a scored set of genes whose GO 
> > annotation is obtained via biomaRt (the full code of the vignette is provided in the
> > inst/doc directory of that package).
> > 
> >  Best wishes
> >   Wolfgang
> 
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Thomas Girke, Ph.D.
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