Vincent,

Thank you for your prompt response. 
I have checked the "oligo" package before. However, it seems lack of functions to infer total copy number, allelic specific and region specific. (I think dChip has such functions, but I can not find R package for dChip).
Could you let me know if there is any function in "oligo" can carry out such tasks?
Thank you.

-Xiaokuan


________________________________
 From: Vincent Carey <stvjc@channing.harvard.edu>

Cc: bioconductor <bioconductor@stat.math.ethz.ch> 
Sent: Saturday, November 26, 2011 8:21 AM
Subject: Re: [BioC] solution for affy human 500k mapping snp array


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.  



e:

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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