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 -- Sent via the guest posting facility at bioconductor.org.

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 at r-project.org] On Behalf Of Raj [guest] Sent: Friday, March 16, 2012 5:36 PM To: bioconductor at r-project.org; drrajan22 at 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 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ 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 IMPORTANT WARNING: This email (and any attachments) is ...{{dropped:9}}

Greetings, You might want to consider using the bioconductor package "GWASTools". I have found it useful for automated detection of baf (ie, B allele Frequency) anomalies (and their graphical presentation) with affy 6.0 data. It would, I think, still require visual inspection of the detected chromosomal anomalies if you want to classify them by copy number changes. Fortunately, there is a function that plots both BAF and Log R Ratio (LRR) for each SNP along a chromosome. Their is a very instructive vignette that accompanies GWASTools. It is called "GWAS Data Cleaning" and can be found via a link from here: http://www.bioconductor.org/packages/release/bioc/html/GWASTools.html I believe that the "GWAS Data Cleaning" document describes the baf anomaly detection methodology and provides detailed code for conducting the analyses, starting on page 40. Cheers, Fred 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 at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Raj [guest] Sent: Friday, March 16, 2012 5:36 PM To:bioconductor at r-project.org;drrajan22 at 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 -- Sent via the guest posting facility at bioconductor.org.

Hi Raj, please check out the cn.farms package for detecting copy number variations in microarray data with a low false discovery rate. For further information about the algorithm and its assessment just drop me an email or get the paper from Nucleic Acids Research: http://nar.oxfordjournals.org/content/early/2011/04/12/nar.gkr197.abst ract Cheers, Okko -- Am 17.03.2012 um 01:35 schrieb Raj [guest]: > > 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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