[BioC] DNA-Methylation, CopyNumber Results

[Ina Hoeschele]

Can someone please clarify for me the need for dye bias adjustment for Illumina Infinium methylation data? Below is an 'explanation' from Illumina to justfy why no dye adjustment is needed: 
""
----- Original Message -----
From: "Sean Davis" <sdavis2 at mail.nih.gov>
To: "Chao-Jen Wong" <cwon2 at fhcrc.org>
Cc: bioconductor at stat.math.ethz.ch
Sent: Thursday, June 17, 2010 5:10:29 PM
Subject: Re: [BioC] DNA-Methylation, CopyNumber Results

On Thu, Jun 17, 2010 at 4:43 PM, Chao-Jen Wong <cwon2 at fhcrc.org> wrote:

> As for Illumina Infinium methylation data, you can use the methylumi
> package to  manipulate the data and perform quality control and
> normalization. Subsequently use limma to do differential methylation
> analysis.
>
>
Just keep in mind that the data from the Illumina arrays are pretty
non-normal, so some assumptions that come into play when using a parametric
testing method may be in question.

Sean



> On 06/16/10 19:22, Noemi Andor wrote:
> > Hi,
> >
> > I need to parse some raw Methylation data from Illumina (Infinium) and
> some copy number results (CGH, high amount of data). I would be grateful for
> any useful information like which bioconducter packages to use, alternative
> tools, normalization.
> >
> > thank's in advance,
> >
> > Noemi
> >
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>
>
> --
> Chao-Jen Wong
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., M1-B514
> PO Box 19024
> Seattle, WA 98109
> 206.667.4485
> cwon2 at fhcrc.org
>
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