Dear Mohamed,

There are two ways to do methylation profiling, one with DMH and other with MeDIP technique. Therefore it is better to provide information of which method you use? In case, DMH, you can go ahead with Limma, as DMH data is linear to methylation level, otherwise use MEDME, which takes care of the non - linear nature of  methyaltion levels generated by MeDIP technique.

Regards,
Prashantha

Lecturer,

Dept. of Biotechnology,

Manipal Life Sciences Center,

Manipal University,

Manipal, India

PIN: 576104

Email:prashantha.hebbar@manipal.edu

Phone: +91-9886359007

--- On Wed, 6/16/10, Mohamed Lajnef <Mohamed.lajnef@inserm.fr> wrote:

From: Mohamed Lajnef <Mohamed.lajnef@inserm.fr>
Subject: [BioC] Agilent CpG islands-Limma
To: bioconductor@stat.math.ethz.ch
Date: Wednesday, June 16, 2010, 1:43 PM

Dear R users,

I  try to use Limma package  to analyze methylation databases generated 
from Agilent CpG Islanfds, but i dont know if this is relevant because  
i have 4 groups ( one replicate for each group) ??
Can you please  suggest me a method to analyze my data ?

Any help will be appreciated
Regards



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