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Nucleic Acids Res. 2013 Apr;41(7):e90. doi: 10.1093/nar/gkt090. Epub 2013 Mar 9.

Low-level processing of Illumina Infinium DNA Methylation BeadArrays.

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Department of Preventive Medicine, USC Keck School of Medicine of USC, Los Angeles, CA 90089, USA.


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.

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