RCP: a novel probe design bias correction method for Illumina Methylation BeadChip

Abstract

Motivation: The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes -- Infinium I (type I) and Infinium II (type II) -- in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis.