[BioC] GO analysis

Ramon Diaz-Uriarte rdiaz at cnio.es
Mon Dec 15 12:33:25 MET 2003

Dear Jose,

You might want to look at our tool


(The paper describing it is in press at Bioinformatics).

It should start working directly with Affy in a week or so. For now, you would 
neet to go to EnsMart, input your list of affy ids, then output the ensemble 
gene names, and input that to fatigo.



On Friday 12 December 2003 18:36, Jose Duarte wrote:
> Hi
> I would like to do some post annotation analysis on my gene list from an
> Affy experiment. Basically we want to see if the set of genes has any
> statistically over represented GO ids in comparison to the total of the
> genes in the chip. An over representation probability should be given to
> each of the categories.
> This is in line with what some packages already do: EASE, GeneMerge,
> GOminer, fatiGO (web)... But I was wondering if somebody did something
> like this already in Bioconductor or maybe it is not a good idea to
> implement this in R as it is not the fastest text searcher.
> Any suggestions welcomed
> Thanks!
> Jose

Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

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