AUTHOR=Xiong Zhuang , Li Mengwei , Ma Yingke , Li Rujiao , Bao Yiming 

TITLE=GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip

JOURNAL=Frontiers in Genetics

VOLUME=Volume 12 - 2021

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.810985

DOI=10.3389/fgene.2021.810985

ISSN=1664-8021

ABSTRACT=Illumina HumanMethylation BeadChip is one of the most cost-effective ways to quantify DNA methylation levels at the single-base level across the human genome, which makes it a routine platform for epigenome-wide association studies. It has accumulated tens of thousands of DNA methylation array samples in public databases, providing great support for data integration and further analysis. However, majority of public DNA methylation data are deposited as processed data without background probes which are widely used in data normalization. Here we present Gaussian mixture quantile normalization (GMQN), a reference based method for correcting batch effects as well as probe bias in HumanMethylation BeadChip. Availability and implementation: https://github.com/MengweiLi-project/gmqn.