title: Low-level processing of Illumina Infinium DNA Methylation BeadArrays.
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.
authors.affiliation: Department of Preventive Medicine, USC Keck School of Medicine of USC, Los Angeles, CA 90089, USA. ttriche@usc.edu
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Triche
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Weisenberger
authors.forename: David
authors.initials: D
authors.lastname: Van Den Berg
authors.forename: Peter W
authors.initials: PW
authors.lastname: Laird
authors.forename: Kimberly D
authors.initials: KD
authors.lastname: Siegmund
mesh_terms: D019175:DNA Methylation; D005456:Fluorescent Dyes; D060148:HapMap Project; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D005456:Fluorescent Dyes