[BioC] Modeling of methylation status using lumi

Ina Hoeschele inah at vbi.vt.edu
Mon Mar 21 20:32:34 CET 2011

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 at 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!


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

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