Hi, We are analyzing our first methylation dataset (Illumina 450k array). Through minfi I am able obtain a list of differential methylated probes (CGxxxx), but I would like to place these in a genomic context. Unfortunately I don't have any hands-on experiences with genome analysis (genomic localization, closest transcript/gene, generating input for genome browser, etc.) so I would appreciate if someone could point my to a workflow that allows these type of analysis starting from a list of probes. I know packages such as GenomicRanges and GenomicFeatures likely can be used for this, but whether these are really the best options, and if so, the exact order/way isn't clear to me yet. Hence, any suggestion is appreciated. Thanks in advance, Guido --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 [[alternative HTML version deleted]]

Just in case you have not seen this (because I think I forgot to describe it in the manual), we now have mapToGenome which easily adds genomic coordinates to your MethylSet. From then on you will be on your own, although we do expect to provide functionality for annotation results "soon" (when we have completed our current task of adding our DMR finder). Kasper On Thu, Oct 11, 2012 at 5:38 PM, Hooiveld, Guido <guido.hooiveld at="" wur.nl=""> wrote: > Hi, > We are analyzing our first methylation dataset (Illumina 450k array). > Through minfi I am able obtain a list of differential methylated probes (CGxxxx), but I would like to place these in a genomic context. Unfortunately I don't have any hands-on experiences with genome analysis (genomic localization, closest transcript/gene, generating input for genome browser, etc.) so I would appreciate if someone could point my to a workflow that allows these type of analysis starting from a list of probes. I know packages such as GenomicRanges and GenomicFeatures likely can be used for this, but whether these are really the best options, and if so, the exact order/way isn't clear to me yet. Hence, any suggestion is appreciated. > > Thanks in advance, > Guido > --------------------------------------------------------- > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld at wur.nl > internet: http://nutrigene.4t.com > http://scholar.google.com/citations?user=qFHaMnoAAAAJ > http://www.researcherid.com/rid/F-4912-2010 > > > [[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