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?
Thanks.
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
"Did you always know?"
"No, I did not. But I believed..."
---Matrix III
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
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.
-w
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
Hi Weiwei,
You're talking about probesets not probes, correct?
Otherwise, you would end up throwing away most of the probes on every
probeset and that would be a fairly bad idea.
You could look at a handful of probes for cases when several probesets
exist for a single gene and see if there are any systematic 3' biases,
but I would expect otherwise. As an alternative you could filter using
variance or interquartile range. It's maybe not as elegant as choosing
the 3' one, but it should work fairly well.
Francois
On Sun, 2007-06-24 at 18:08 -0400, Weiwei Shi wrote:
> 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.
>
> -w
>
> 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
> >
>
>
