Updated 04/03/2013 by Roderick
Welcome to Non Scientia. The platform I mainly use (next to Epityper) for measuring DNA methylation is the Illumina 450k array. There are that many packages; if you are a beginner you are overwhelmed by the number of packages available. Here I try to give an overview of available packages and latest 450k literature.
450k array design
The analysis of 450 methylation data is complicated by the presence of two types of probes:type I and type II. Type I uses two types of beads that measure the methylated and unmethylated signal separately but within one color channel, either red or green. Type II probes however, use only one bead but two different color channels, red and green for the unmethylated and methylated signal. However, this is where the normalization can help you out: it can make the distributions of the probe types more similar.
Figure without permission (booo!) adapted from Science Direct. Bibikova et al.