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

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