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