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 Human-Methylation450, 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. © 2013 The Author(s).
CITATION STYLE
Triche, T. J., Weisenberger, D. J., Van Den Berg, D., Laird, P. W., & Siegmund, K. D. (2013). Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Research, 41(7). https://doi.org/10.1093/nar/gkt090
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