Low-level processing of Illumina Infinium DNA Methylation BeadArrays

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…

• WU
  Washington University in St. Louis
• NI
  National Institutes of Health

  Awards: U24 CA143882, CA097346, P30 ES07048, P01 CA101937