On Jan 1, 2012 3:02 AM, <bioconductor-request@r-project.org> wrote: > > Send Bioconductor mailing list submissions to > bioconductor@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/bioconductor > or, via email, send a message with subject or body 'help' to > bioconductor-request@r-project.org > > You can reach the person managing the list at > bioconductor-owner@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioconductor digest..." > > > Today's Topics: > > 1. mapping snp array probe to a gene, biomaRt or others? > (Xiaokuan Wei) I usually pull gene boundaries from a biomaRt and put them in a RangedData object (from the IRanges package). If your snps are similarly organized, then the findOverlaps function will get you a reasonable answer. The genoset package has a better way to summarize copy number by gene, given a RangedData of gene boundaries. Please check out the end of the genoset vignette. Regards, Pete Haverty > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 31 Dec 2011 15:19:06 -0800 > From: Xiaokuan Wei <weixiaokuan@yahoo.com> > To: bioconductor <bioconductor@stat.math.ethz.ch> > Subject: [BioC] mapping snp array probe to a gene, biomaRt or others? > Message-ID: > <1325373546.55508.YahooMailNeo@web114208.mail.gq1.yahoo.com> > Content-Type: text/plain > > Dear List: > > Happy New Year! > > I have a question regarding mapping the gene to a copy number variations. > > I have affy 250 nsp mapping arrays results. Now I try to map the result for each probe to a gene. > then, I can perform correlation analysis between the copy number variation and gene expression level for candidate genes. > > I think I have an idea to map expression levels to each gene; but I don't know how to map copy number variation values to each gene. > Should I just parse the annotation file of "Mapping250K_Nsp.na32.annot.csv" to match each probe to a gene symbol? or there are some other ways. > Which tools would you recommend? > > Any suggestion will be appreciated. Thank you. > > -Xiaokuan > [[alternative HTML version deleted]] > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 107, Issue 1 > ******************************************** [[alternative HTML version deleted]]