Hi Ina and Tim

For the methylation call part, I haven't work on that for a while because
there are other priorities.

For the color bias adjustment of 450K array, you need to use the development
version, which perform color bias adjustment for both type I and II designs.
Basically, it estimates the color bias based on type I design (methylated
and unmenthylated measurements of the same CpG-site has  the same color),
which is the same as Infinium 27k, and then use the fitted curve to adjust
probes with type II design (methylated and unmenthylated measurements of the
same CpG-site has different colors).


Pan


Date: Mon, 13 Jun 2011 18:05:16 -0400
From: Ina Hoeschele <inah@vbi.vt.edu>
To: Tim Rayner <tfrayner@gmail.com>
Cc: Bioconductor <bioconductor@stat.math.ethz.ch>
Subject: Re: [BioC] lumi, Illumina Methylation 450k,    and robust
       methylation calls
Message-ID: <9267536a-70f6-4582-a38f-
8d2288c2afed@zimbra>
Content-Type: text/plain; charset="utf-8"

<<
I have recently started to use the lumi package to analyse some
Illumina Human Methylation 450k data, and I have run into some
problems which seem to revolve around division by zero in the
gammaFitEM() function. I have adjusted the colour balance and quantile
normalised as suggested in the vignette
>>

Hi Pan and Tim (et al),
  this is in regard to an earlier email from Tim - is the colour balance
adjustment performed for ALL probes or only for probes with Infinium I
assay? Is the quantile normalization done for both Inf I and II together
(rather than separately) in the current (development) version of lumi? I
would be reluctant to do it that way, and I apologize if this is described
somewhere and I misssed this informaiton.
Thanks, Ina

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