[BioC] R: C. elegans annotation package

Alberto Goldoni alberto.goldoni at eurogene.org
Tue Jul 5 10:27:01 CEST 2005

Try this one:



i hope this is helpful for you!


Dr Alberto Goldoni

Medical Genetics Unit

S. Orsola-Malpighi Hospital

Via Massarenti n.9, Pad 11

40100 Bologna, Italy

Mobile Phone: +39-338-4145970

Fax: +39-051-636-4004

alberto.goldoni at eurogene.org

-----Messaggio originale-----
Da: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Per conto di James W.
Inviato: lunedì 4 luglio 2005 20.48
A: Emmanuel Levy
Cc: bioconductor at stat.math.ethz.ch
Oggetto: Re: [BioC] C. elegans annotation package

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'.


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).



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

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