[BioC] map probe to refseq and select 3' biased one

Sean Davis sdavis2 at mail.nih.gov
Sun Jun 24 23:22:48 CEST 2007

Weiwei Shi wrote:
> Hi,
> Does anyone know how to map affy probe to refseq and select 3'biased
> one, so probe to gene can be one to one?
Are you talking about an affy probeset, or just the probes?  Even if you 
map to refseq, there are multiple refseqs per gene in many cases, and 
some of them have the same 3' exon.  Unfortunately, one simply has to 
deal with this many-to-many situation.

To answer your question, though, in general mapping probes or probesets 
to other sequences will involve using blast, blat, or some other 
alignment tool.  Going down this road, particularly with affymetrix 
arrays, is a fairly large undertaking; I would not advise it unless you 
have a particularly compelling reason to do so.


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