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
>
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