[BioC] Affy SNP array analysis

Garrett Frampton fcalive at hotmail.com
Fri Sep 12 10:35:37 MEST 2003


	We ran some 10K SNP Chips last week during training at the Boston
University Microarray Core Facility
(http://www.bu.edu/genome/microarray/index.htm). They seem like a very good
product and Affymetrix will be coming out with a 100K SNP chip next year.
Pretty cool.  On the downside (though it will give us something to do) the
algorithms for determining SNP calls are just as screwy as the algorithms
from the expression chips.  Good luck.

Garrett Frampton

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Holger
Sent: Thursday, September 11, 2003 6:55 PM
To: bioconductor at stat.math.ethz.ch
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Affy SNP array analysis

I think this is a very interesting idea, and I might probably contribute to
such a package since I'm currently working on a project that is concerned
with SNP data (mainly cluster and classification analysis, no SNP
But I'm only interested in co-authoring such a package. So if anyone else is
interested in making a package for SNP analysis, please send me an email.

I have already written some function, but I've just started.

> >
> > As you may or may not know, Affy now has an array for SNP mapping. Are
> > there plans to make a package for analyzing this sort of data, or is
> > this too far afield from gene expression to fall under the Bioconductor
> > umbrella?
> I would say this is less a question of falling under an umbrella
> (Bioconductor is directed at general computational biology) and more
> a question of resources.  We have a lot of work to do to stabilize
> and deploy the next release.
> I have yet to see data from these SNP chips;
> if there are any public resources that will help us to consider
> class design and basic strategies, please let us know.  The
> genotyping chips are probably a good opportunity for someone
> looking to make an impact on the project.
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