[BioC] affy package pm ids and position on mRNA

Laurent Gautier laurent at cbs.dtu.dk
Fri Aug 29 11:58:38 MEST 2003

On Wed, Aug 27, 2003 at 03:18:34PM +0100, Keith Vass wrote:
> Hi all
> I have used affy to get perfect-match probe data for a number of affy
> HG-U133a chips and I get the probes as follows 210298_x_at1, 210298_x_at2
> etc
> How do I find out what the mapping is to the oligodata that Affymetrix
> give for their probes as I want to know the position the oligos bind to in
> the sequence as this is a gene with an alt-splicing site?
> Look forward to your reply.
> Keith
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr J Keith Vass
> Bioinformatics Unit, 
> Cancer Research UK Beatson Institute
> Garscube Estate
> Bearsden
> Glasgow G61 1BD
> eMail k.vass at beatson.gla.ac.uk
> FAX (44) (0)141 942 6521
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Hi Keith,
I did this kind of job with Affymetrix chips very recently
(and I have a something submitted about the study).
There is a documentation on its way where I detail all the steps and
intermediate results (no yet complete, hence not yet fully public).
In the meanwhile, I'd be happy to try to help you off-list if you wish. 

As a first step, you may want to get the packages Biobase
(devel-version), matchprobes (in the 'devel' section) and splicegear
(also in the 'devel' section - for a reason I still did not elucidate
it does not build for Windows there, if you need the MSWindows version
try http://www.cbs.dtu.dk/laurent/download/splicegear/ ).



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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent

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