I can't comment on popularity, but the vignetttes listed at

http://www.bioconductor.org/packages/release/bioc/html/oligo.html

address processing of these arrays for genotyping.

On Fri, Nov 25, 2011 at 10:26 PM, Xiaokuan Wei <weixiaokuan@yahoo.com>wrote:

> Dear list,
>
> I am trying to analyze a set of affy human 500k mapping snp arrays. I try
> to make copy number calls and relate them to candidate genes.
> I am wondering: what is the most popular package for such a task?
>
>
> Thank you.
>
> Xiaokuan
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>
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