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 [[alternative HTML version deleted]]

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 > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

You might also try the GWASTools package. See the section "chromosome anomaly detection" in the Data Cleaning vignette, and the "Preparing Affymetrix Data" vignette for how to format SNP 6.0 data for use with GWASTools. Stephanie On 5/30/12 3:00 AM, bioconductor-request at r-project.org wrote: > Message: 16 > Date: Tue, 29 May 2012 10:04:07 -0700 > From: Valerie Obenchain<vobencha at="" fhcrc.org=""> > To: Rajan Saini<drsaini22 at="" yahoo.com=""> > Cc:"bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] Package for doing Copy number analsysi with LOH > Message-ID:<4FC50187.9080601 at fhcrc.org> > Content-Type: text/plain > > 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 >> > [[alternative HTML version deleted]] >> > >> > >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives:http://news.gmane.org/gmane.science.biology. informatics.conductor

If you have paired tumor-normal data, packages aroma.affymetrix and PSCBS will do this for you. /Henrik On Thu, May 17, 2012 at 6:39 PM, Rajan Saini <drsaini22 at="" yahoo.com=""> 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 > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor