A good place to start looking is the biocViews tree,

http://bioconductor.org/packages/release/BiocViews.html#___Software

These packages might be useful  cn.farms, cn.mops, genoset, SNPchip, 
snpStats, ...

Valerie


On 05/17/2012 06:39 PM, Rajan Saini wrote:
> Dear Bioconductor community,
>   
>     I am looking for a package that does Copy number along with LOH analysis (B allele frequency) for intensity files from SNP 6.0 arrays. Please direct me to the right package for this kind of analysis. Thank you very much in advance
>   
>   
> Raj
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>
>
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