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.

Results

Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type b

SUBMITTER: Niu L 

PROVIDER: S-EPMC5013906 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature