[BioC] GO analysis

Lawrence Paul Petalidis lpp22 at cam.ac.uk
Fri Dec 12 19:22:24 MET 2003

Try onto-express. I like it quite a lot.
Intelligent Systems and Bioinformatics Laboratory

Yours, Lawrence

Lawrence Paul Petalidis 
Ph.D. Candidate

University of Cambridge
Department of Pathology

-----Original Message-----
From: bioconductor-bounces+lpp22=cam.ac.uk at stat.math.ethz.ch
[mailto:bioconductor-bounces+lpp22=cam.ac.uk at stat.math.ethz.ch]On Behalf
Of Jose Duarte
Sent: 12 December 2003 17:37
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] GO analysis


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



Jose Duarte
MRC Functional Genetics Unit
Department of Human Anatomy and Genetics
University of Oxford
South Parks Road
Oxford OX1 3QX
Phone: +44 (0)1865 282650
e-mail: jose.duarte at anat.ox.ac.uk

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