Hi Pelizzola, You have mentioned in your paper (Pelizzola et al, Genome.Res 2008) that DNA methylation data is not linear and you have used limma in your data analysis. So i want to know have you fitted lmFit() on your data? If so how MEDME will make change over linear modeling fitted data ? If i am wrong any where please excuse me. Thankfully A.Ashwin Departement of Biotechnology MLSC Manipal University INDIA [[alternative HTML version deleted]]

Hi, in the paper you can find that the MeDIP-chip enrichment is not linearly related with the DNA methylation level. MEDME is able to model this non-linear relationship using a calibration dataset where the genomic DNA is fully methylated. Limma is not used in MEDME. The only point where limma is mentioned in the paper is for the array data normalization. In this regard, enrichment data analyzed with MEDME should be already normalized by the user. I hope this helps, mattia ---------- Forwarded message ---------- From: Ashwin Kumar <ashwin.havoc@gmail.com> To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> Date: Thu, 23 Apr 2009 16:36:31 +0530 Subject: [BioC] assistance to understand MEDME Hi Pelizzola, You have mentioned in your paper (Pelizzola et al, Genome.Res 2008) that DNA methylation data is not linear and you have used limma in your data analysis. So i want to know have you fitted lmFit() on your data? If so how MEDME will make change over linear modeling fitted data ? If i am wrong any where please excuse me. Thankfully A.Ashwin Departement of Biotechnology MLSC Manipal University INDIA