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 [[alternative HTML version deleted]]