Hi Weili

You can check the "methylumi" package for the methylation data input file
format information, and the developing version of "lumi" package for the
preprocessing of Infinium 450K methylation data.

Pan

Date: Thu, 21 Jul 2011 11:54:52 +0800
From: weili yan <01.weili@gmail.com>
To: <bioconductor@stat.math.ethz.ch>
Subject: [BioC] how to get the LIMMA required files for analysis from
       Illumina Methylation450K chip assay
Message-ID:
       <CAEqrnaftEL-O1+Qa7OzoXOL+2ESC_QFZgGj-amKY70Lz9oui0Q@mail.gmail.com>
Content-Type: text/plain

Dear Sir,
We performed a genomewide methylation assay among a 6:6 case-control sample.
It is a two-colour signal data. We got 4 data files after the data analysis
by using Illumia GenomeStudio-Methylation software.
My question is how can I extract data files required by LIMMA?
I hope to genotype the differential loci indicated by the discovery array in
a larger sample, and perform association analysis between methylation status
or degree with quantitative or qualitative phenotypes. LIMMA is no doubt the
right tooll to do this.
However, we got problems in transfering Illumia data files to LIMMA.

Do you have any training or online learning materials about this? How can I
get help from you?


Best wishes

Weili

--
WeiliYan, PhD, Director
Department of Clinical Epidemiology
Children's Hospital of Fudan University
399 Wanyuan Road
Minhang District, Shanghai 201102
Tel&Fax: (86) 21 64931215

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