[BioC] hypergeometric enrichment of GO terms

[Wolfgang Huber]

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