As Sean noted, exporting the data from GenomeStudio with an up-to-date 450k manifest is a perfectly reasonable way to annotate your results if you are not pumping them directly into a package like GeneAnswers (or similar packages that expect deeper integration). If someone wants to help beta test a 450k annotation package, I'm not opposed to making it available, with the understanding that it is not yet Bioconductor release quality. The idea would be to tie up any loose ends related to documentation of certain new mapping fields, and thus get the documentation and integration up to the expectations of BioC users. The core Bioconductor developers have been extremely generous with their time in helping me get up to speed and I'd like to hear what they think about such an idea before proceeding. Depending on how you process, export, and annotate the results of a given 27k or 450k experiment, it's possible to end up with diverging results. This bothered me, so I wrote a package to decouple the preprocessing from GenomeStudio and focus on IDAT files (pretty much the same way that CEL files are standard for Affymetrix output). The codebase for processing 27k/450k chips from raw IDAT files is available from GitHub. I could post updated annotations there as well: https://github.com/ttriche/methylumIDAT Please note that the above codebase is not up to Bioconductor standards yet. In particular, all but the most critical user-facing functions are undocumented, save for comments. Once the package gets more documentation and testing, I hope to merge it into methylumi, and with any luck that should happen before the next major release. Some of the generic functions should probably be merged sooner, so I'll try sending a pull request or some patches and get those into the development version of methylumi this week. --t On Tue, Feb 15, 2011 at 3:48 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Tue, Feb 15, 2011 at 6:42 AM, Dario Greco <dario.greco@helsinki.fi> >wrote: > > > Dear friends. > > i am starting the analysis of a set of Infinium Human Methylation 450k > > beadchips and I would like to run the analysis with lumi/methylumi. > > i have seen track in mailinlist of a possible update back during last > fall. > > what is the situation at the moment? apparently, there is not yet an > > annotation package for the infinium 450k. > > > > Hi, Dario. There is not one publicly available right now, no. That said, > if you do your genomestudio export with all the annotation columns, those > are loaded by methylumi, so the annotation comes along for the ride by > default. We hope to have an annotation package in place for the next > release. > > Sean > > [[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 > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]

While the thread is running, we will also be using these chips, can anyone tell me their experiences: Am I correct that it is the ratio of Methyation probes/ Unmethylated probe that provides the methylated signal like the Infinium Methylation Assay? So the metric then a ratio between 0-1 ? What are typical within-class variances for a "region" (so I might estimate sample size)? Thanks Paul -----Original Message----- From: Sean Davis <sdavis2@mail.nih.gov> To: Dario Greco <dario.greco@helsinki.fi> Cc: bioconductor@r-project.org Subject: Re: [BioC] Infinium Human Methylation 450k Date: Tue, 15 Feb 2011 06:48:40 -0500 On Tue, Feb 15, 2011 at 6:42 AM, Dario Greco <dario.greco@helsinki.fi>wrote: > Dear friends. > i am starting the analysis of a set of Infinium Human Methylation 450k > beadchips and I would like to run the analysis with lumi/methylumi. > i have seen track in mailinlist of a possible update back during last fall. > what is the situation at the moment? apparently, there is not yet an > annotation package for the infinium 450k. > Hi, Dario. There is not one publicly available right now, no. That said, if you do your genomestudio export with all the annotation columns, those are loaded by methylumi, so the annotation comes along for the ride by default. We hope to have an annotation package in place for the next release. Sean [[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]]