[BioC] annaffy annotation

James W. MacDonald jmacdon at med.umich.edu
Wed Jan 4 22:47:36 CET 2006

Stephanie Mewborn wrote:
> I'm not sure of the best way to ask this question, but I'll try.  I 
> used anncols and anntable within R to annotate my final list of up/down 
> genes from my array analysis.  I am using subsequent programs to look 
> at these genes that use the Hs.xxxx unigene identifier to look up 
> additional information for each gene.  Some of the Hs.xxx numbers 
> assigned to the affymetrix probe ids during the annotation now produce 
> errors in my further analyses.  When I look these ids up at Unigene I 
> get a message that the id has been retired.  Is there a better way to 
> have this table annotated so that it is more current with the UniGene 
> database?

Are you using the most current version of the annotation package for 
your Affy chip? These were re-built only a few months ago, so I wouldn't 
expect many UniGene IDs to have been retired in the interim.



> Stephanie
> Stephanie K. Mewborn, Ph.D.
> Post-Doctoral Fellow
> University of Chicago
> Department of Medicine, Section of Cardiology
> Phone:  773-702-2684
> Fax:  773-702-2681
> 	[[alternative text/enriched version deleted]]
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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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