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

Weiwei Shi helprhelp at gmail.com
Mon Jun 25 00:08:52 CEST 2007

Intially I thot I could tell from e.g. hgu133aREFSEQ. However, I did not find.

The reason I do this, is following MAQC I paper when they align
different probes from different platforms. Currently I am focusing on
affy products (still not the same platforms). I was notified that they
selected 3'bias in this many2one situation.

I believe there exists some RefSeq database which has that field to
tell you which probe (for the same gene) is the 3' end (though not
sure of it). Since today is Sunday I don't want to bother people, so I
try to post here to see if there is a solution or not.


On 6/24/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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.
> Sean

Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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