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- Title
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.
- Authors
Liang Niu; Zongli Xu; Taylor, Jack A.
- 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 bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ.
- Subjects
METHYLATION; GENOME editing; MOLECULAR probes; MOLECULAR biology techniques; MOLECULAR structure; BIOCHEMISTRY
- Publication
Bioinformatics, 2016, Vol 32, Issue 17, p2659
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btw285