[BioC] solution for affy human 500k mapping snp array
beniltoncarvalho at gmail.com
Sun Nov 27 00:42:05 CET 2011
oligo doesn't offer a copy number tool (yet). However, the results you
get from snprma() (summaries for alleles A and B) are the starting
point for copy number analysis, which may be of use for you (note that
total copy numbers are often estimated from alleleA+alleleB).
On 26 November 2011 20:46, Xiaokuan Wei <weixiaokuan at yahoo.com> wrote:
> 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.
> From: Vincent Carey <stvjc at channing.harvard.edu>
> Cc: bioconductor <bioconductor at 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
> address processing of these arrays for genotyping.
> 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?
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