[BioC] GO over representation analysis

[michael watson (IAH-C)]

Dear All

I think one thing that is frustrating here is that there is not a simple
guide here for people who want to create an annotation package for an
array that does not yet have one.

Do we use AnnotationDbi?  Or AnnBuilder?  Or is there another way?

What is the "best practice" for building an annotation package?

Thanks
Mick 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marc
Carlson
Sent: 25 August 2008 17:03
To: Heike Pospisil
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GO over representation analysis

You could just make an annotation package for the array in question by 
using the SQLForge code in the AnotationDbi package.
You can find instructions on how to do this here:

http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html

Let me know if you have any questions about SQLForge.


  Marc



Heike Pospisil wrote:
> Hello Bioconductors,
>
> I am looking for a method to perfom over representation analysis (Gene

> Ontology) within R. I have data from the Maize Oligonucleotide Array
(two 
> channel) with the GO categories for all probes on this array. I have 
> clustered the genes using Maanova and I am interested in GO over 
> representation of the gene lists from these clusters.
>
> I know the GO tools from Bioconductor (e.g. GOstats), but I do not
know how to 
> adapt the analysis to an 'unusual' array with no annotation data
package and 
> now Entrez IDs. Any hints?
>
> Thanks in advance,
> Heike
>

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