[BioC] Copy number analysis

[Valerie Obenchain]

In a more general sense (i.e., maybe useful for future searches), a 
listing of all BioC packages with a "copy  number variants" tag in the 
DESCRIPTION file use the BiocViews tree,

     
http://bioconductor.org/packages/2.9/BiocViews.html#___CopyNumberVariants

Valerie


On 03/16/2012 07:28 PM, Mete Civelek wrote:
> You can try aroma.affymetrix. Information specific to SNP 6.0 is located at
> http://www.aroma-project.org/chipTypes/GenomeWideSNP_6
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Raj [guest]
> Sent: Friday, March 16, 2012 5:36 PM
> To: bioconductor at r-project.org; drrajan22 at yahoo.com
> Subject: [BioC] Copy number analysis
>
>
> Dear Bioconductor community,
>
>    I am looking for a package for Copy number analysis using CEL file that I
> have obtained from Affy SNP 6.0. I have CHP files from birdseed. Now I want
> to analyze my data for Copy number and Loss of heterozygosity (using B
> allele frequency) and find regions of CN alterations and LOH with or without
> Copy number changes. Can anyone direct me to the correct package available
> for this?
>
>   -- output of sessionInfo():
>
> R studio
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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