[BioC] GO enrichment for genome-wide analysis

Ting-Yuan Liu tliu at fhcrc.org
Tue Jan 10 19:34:53 CET 2006

Hi Burak,

If you use the whole-genome annotation package (such as YEAST) in the 
GOHyperG function, you should get what you want.  

Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA

On Tue, 10 Jan 2006, burak kutlu wrote:

>  Hi,
>  My understanding is that GOstats implements the GO term enrichment analysis for studies using microarrays (where the lib argument is passed to "GOHyperG" to define the microarray-specific environment, therefore the gene universe).
>  I was wondering if there is a readilly-available function for determining GO term significance that uses the GO terms from the whole genome rather than the GO terms from the genes represented on an array. Please point me to this function if I have failed to find it in the documentation.
>  Thanks 
>  -Burak Kutlu
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