[BioC] C. elegans annotation package

[James W. MacDonald]

Emmanuel Levy wrote:
> Hello,
> I would like to analyse some C. elegans affimetrix chips. I couldn't find
> an annotation package linking gene ids to description, go term, chromosome
> location, etc ... how long do you think it might take to create one?
> (given that I don't know the process at all and that no one in the lab can
> help me). Or, is there any way around?
> Thank you very much in advance for your help/suggestions,
> Emmanuel

My experience with C. elegans is that the annotation is woefully 
incomplete. Before you spend the time and effort to building an 
annotation package, you might simply download the annotation file from 
Affy and do things 'by hand'.

http://www.affymetrix.com/Auth/analysis/downloads/taf/Celegans_annot_csv.zip

You can import this file into R using read.csv(), and then annotate your 
list of significant genes. You can use htmlpage() in the annotate 
package to output an HTML table with links to various online databases 
(see the prettyOutput vignette).

HTH,

Jim


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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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