Batch effect correction for genome-wide methylation data with Illumina Infinium platform.

ABSTRACT:

Background

Genome-wide methylation profiling has led to more comprehensive insights into gene regulation mechanisms and potential therapeutic targets. Illumina Human Methylation BeadChip is one of the most commonly used genome-wide methylation platforms. Similar to other microarray experiments, methylation data is susceptible to various technical artifacts, particularly batch effects. To date, little attention has been given to issues related to normalization and batch effect correction for this kind of data.

Methods

We evaluated three common normalization approaches and investigated their performance in batch effect removal using three datasets with different degrees of batch effects generated from HumanMethylation27 platform: quantile normalization at average β value (QNβ)

SUBMITTER: Sun Z 

PROVIDER: S-EPMC3265417 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature