Title: Low-level processing of Illumina Infinium DNA Methylation BeadArrays.
Authors: Triche Jr, Timothy J; Weisenberger, Daniel J; Van Den Berg, David; Laird, Peter W; Siegmund, Kimberly D
Published In Nucleic Acids Res, (2013 Apr)
Abstract: We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal. Our approach capitalizes on a new use for the Infinium I design bead types to measure non-specific fluorescence in the colour channel opposite of their design (Cy3/Cy5). This provides tens of thousands of features for measuring background instead of the much smaller number of negative control probes on the platforms (n = 32 for HumanMethylation27 and n = 614 for HumanMethylation450, respectively). We compare the performance of our methods with existing approaches, using technical replicates of both mixture samples and biological samples, and demonstrate that within- and between-platform artefacts can be substantially reduced, with concomitant improvement in sensitivity, by the proposed methods.
PubMed ID: 23476028
MeSH Terms: DNA Methylation*; Fluorescent Dyes; HapMap Project; Humans; Oligonucleotide Array Sequence Analysis/methods*