[Bioc-devel] Gene Annotation and Gene Ontology

[Steve Lianoglou]

Hi Zhiyou,

On Wed, May 12, 2010 at 9:16 AM, Dr Z. Du <zd224 at cam.ac.uk> wrote:
> Hi,
>
> I finished analysis of the differential expression of genes using Limma
> package, and got the list of differentialy expressed genes. I tried to make
> gene annotation (ath1121501db)and Gene ontology (gostats) for these
> differential expressed genes. But, I failed. Does anybody have any
> experience about is, and share it with me? I need to say the microarray I
> used is Affy Arabidopsis ATH1. I will appreciate if you can supply any
> information.

This question doesn't really belong on bioc-devel: you should repost
to the general user/helpl list:

Sign up at: https://stat.ethz.ch/mailman/listinfo/bioconductor
email: bioconductor at stat.math.ethz.ch

That having been said, it might help to add more information to your
question. You said that you tried and failed to do GO analysis with
GOstats, but what did you try to do, exactly? What error messages are
you getting?

The "GOstatsHyperG" vignette should pretty much take you from start to
finish w/ what you want to do. In section 2.2: "Gene selection via
t-test", you are rather doing your gene selection by using limma to
pick off the differentially expressed genes ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact