[BioC] solution for affy human 500k mapping snp array

[Benilton Carvalho]

Xiaokuan,

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).

b

On 26 November 2011 20:46, Xiaokuan Wei <weixiaokuan at yahoo.com> wrote:
> 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 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
>
> 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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>>
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