[BioC] Multiple genes per probeset

[James MacDonald]

http://article.gmane.org/gmane.science.biology.informatics.conductor/25621/match=multiple+probeset

Richard Friedman wrote:
> Dear Bioconductor list,
> 
>     Some time ago I downloaded a Mouse annotation database from the 
> Affymetrix web site (Version 29 according to my notes).
> It occasionally contains more than one gene per probeset separated by 3 
> slashes. For example for the probeset
> 1415691_at the genes listed are Dlg1 /// LOC100047603. Presumably this 
> is because the probeset is found to have
> specificity for more than one gene.
> 
>     When I get the annotation from mouse4302.db (version  2.2.11) using 
> the annaffy package I get only one gene
> per probeset for those probesets that have more than one gene in the 
> Affy package. For example, for the case of
> 1415691_at it only lists Dig1.
> 
>     Is this because reannotation and mapping has found the gene most  
> for which the probeset is most specific?
> If that is the case can you point me at a reference as to how this is done?
> The paper  Dai et al. Evolving gene/transcript definitions significantly 
> alter the interpretation of GeneChip data. Nucleic Acids Res. 2005 Nov 
> 10;33(20):e175. deals with this issue, but as best I can understand it 
> they assign different probeset names.
> 
>     Or should there be multiples genes per probeset on output?
> 
> Thanks and best wishes,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
> 
> In Memoriam,
> Philip Klass
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
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734-615-7826
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