Hi Raj,   In addition to aroma, there's also copy number estimation in crlmm and a hidden Markov model in VanillaICE that incorporates log R ratios and BAFs. 

Rob

On Mar 17, 2012, at 7:00 AM, bioconductor-request@r-project.org 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@r-project.org
> [mailto:bioconductor-bounces@r-project.org] On Behalf Of Raj [guest]
> Sent: Friday, March 16, 2012 5:36 PM
> To: bioconductor@r-project.org; drrajan22@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


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