Hi Pan, have you received methylation 450K data? We have begun producing these data and are wondering about the status of the lumi package? Many thanks, Ina ----- Original Message ----- From: "Pan Du" <dupan@northwestern.edu> To: "Gilles Gasparoni at googlemail.com" <gillesgasparoni at="" googlemail.com="">, bioconductor at r-project.org Cc: "Manuel Mayhaus" <manuel.mayhaus at="" uks.eu="">, "Sabrina Pichler" <brina23 at="" gmx.de="">, "Thomas Feulner" <thomas.feulner at="" uniklinikum-="" saarland.de="">, "Caterina Riehle" <caterina.riehle at="" tum.de=""> Sent: Wednesday, December 15, 2010 2:33:18 PM Subject: Re: [BioC] Modeling of methylation status using lumi Hi Gilles Thanks for your feedback of the newly implemented Methylation functions in the lumi package. As for the functions of modeling methylation status, I will organize and upload them to the developing version within next few weeks, hopefully by the end of this year. For the Illumina 450k methylation chip, we haven't got the data yet. Hopefully, we will get two batches of 450k data within about next two months, I will update functions to handle the 450k data at that time. If you have 450k data and would like to share, I can update the package earlier. Happy holidays! Pan On 12/15/10 5:30 AM, "Gilles Gasparoni at googlemail.com" <gillesgasparoni at="" googlemail.com=""> wrote: > Dear Dr. Du, > > my name's Gilles Gasparoni, I'm a post-doc working in the clinics of > psychiatry at the Saarland University, Germany. We are working in the > field of Alzheimer's disease and recently started an epigenetic > project. We analysed DNA methylation of numerous post-mortem brain > tissues (3 different brain areas) using bisulfite converted DNA on the > 27K Infinium Methylation array. > We highly appreciated your publication of the wonderful lumi package, > which we have used to evaluate the generated data. Now, we're at the > point, where we would like to use your lumi package to model the > methylation status (which is referred to 3.9 in your manual "analyze > illumina infinium methylation microarray data"...to be added soon). > Since we're a bit stuck at this point of our data analysis I would > like to ask you if you are planning to publish this features soon? > Otherwise, are you able to give a kind of beta-version of this feature? > > Another question is reffering to the recently announced 450K > methylation chip from illumina: are you also planning to support this > chip with your lumi-package? > > thank a lot for your help!!!! > > best regards, > > > Gilles Gasparoni _______________________________________________ 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

Thanks. Ina Yes, we also got some 450k data. But I have no time to work on it yet because I am busy with moving. The current lumi package should be able to processing 450k data. And I believe Tim Triche will produce the annotation package for 450k methylation data in the new Bioc release. Pan On Mon, Mar 21, 2011 at 2:32 PM, Ina Hoeschele <inah@vbi.vt.edu> wrote: > Hi Pan, > have you received methylation 450K data? We have begun producing these > data and are wondering about the status of the lumi package? > Many thanks, Ina > > > > ----- Original Message ----- > From: "Pan Du" <dupan@northwestern.edu> > To: "Gilles Gasparoni@googlemail.com" <gillesgasparoni@googlemail.com>, > bioconductor@r-project.org > Cc: "Manuel Mayhaus" <manuel.mayhaus@uks.eu>, "Sabrina Pichler" < > brina23@gmx.de>, "Thomas Feulner" <thomas.feulner@uniklinikum- saarland.de="">, > "Caterina Riehle" <caterina.riehle@tum.de> > Sent: Wednesday, December 15, 2010 2:33:18 PM > Subject: Re: [BioC] Modeling of methylation status using lumi > > Hi Gilles > > Thanks for your feedback of the newly implemented Methylation functions in > the lumi package. As for the functions of modeling methylation status, I > will organize and upload them to the developing version within next few > weeks, hopefully by the end of this year. For the Illumina 450k methylation > chip, we haven't got the data yet. Hopefully, we will get two batches of > 450k data within about next two months, I will update functions to handle > the 450k data at that time. If you have 450k data and would like to share, > I > can update the package earlier. > > Happy holidays! > > > Pan > > > On 12/15/10 5:30 AM, "Gilles Gasparoni@googlemail.com" > <gillesgasparoni@googlemail.com> wrote: > > > Dear Dr. Du, > > > > my name's Gilles Gasparoni, I'm a post-doc working in the clinics of > > psychiatry at the Saarland University, Germany. We are working in the > > field of Alzheimer's disease and recently started an epigenetic > > project. We analysed DNA methylation of numerous post-mortem brain > > tissues (3 different brain areas) using bisulfite converted DNA on the > > 27K Infinium Methylation array. > > We highly appreciated your publication of the wonderful lumi package, > > which we have used to evaluate the generated data. Now, we're at the > > point, where we would like to use your lumi package to model the > > methylation status (which is referred to 3.9 in your manual "analyze > > illumina infinium methylation microarray data"...to be added soon). > > Since we're a bit stuck at this point of our data analysis I would > > like to ask you if you are planning to publish this features soon? > > Otherwise, are you able to give a kind of beta-version of this feature? > > > > Another question is reffering to the recently announced 450K > > methylation chip from illumina: are you also planning to support this > > chip with your lumi-package? > > > > thank a lot for your help!!!! > > > > best regards, > > > > > > Gilles Gasparoni > > _______________________________________________ > 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]]