Hi , I would like to get some inputs on analyzing copy number variants for a case control study. I have never worked with copy number variants before and I was wondering if there are any R packages out there for analyzing copy number variants data and to get me started. I do have cell files from Affymetrix for my cases and controls. I appreciate your inputs and help Thanks [[alternative HTML version deleted]]

there are various possibilities, but crlmm package does include a vignette called copynumber.pdf that should be useful. On Wed, May 12, 2010 at 7:33 PM, Kay Jaja <kjaja27@yahoo.com> wrote: > Hi , > > I would like to get some inputs on analyzing copy number variants for a > case control study. > I have never worked with copy number variants before and I was wondering if > there are any R packages out there for analyzing > copy number variants data and to get me started. I do have cell files from > Affymetrix for my cases and controls. > > I appreciate your inputs and help > Thanks > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Dear Kay, You might want to look at CNVassoc. The method is described here Gonzalez J, Subirana I, Escaramis G, Peraza S, Caceres A, Estivill X, Armengol L. Accounting for uncertainty when assessing association between copy number and disease: a latent class model. BMC Bioinformatics 2009; 10:172+. And the package is available from http://www.creal.cat/jrgonzalez/software.htm#ancla-cnvassoc Best, R. On Thursday 13 May 2010 01:33:11 Kay Jaja wrote: > Hi , > > I would like to get some inputs on analyzing copy number variants for a > case control study. I have never worked with copy number variants before > and I was wondering if there are any R packages out there for analyzing > copy number variants data and to get me started. I do have cell files from > Affymetrix for my cases and controls. > I appreciate your inputs and help > Thanks > > > > [[alternative HTML version deleted]] > -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-732-8000 ext. 3019 Fax: +-34-91-224-6972 **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:7}}