Complete Pipeline for Infinium ® Human Methylation 450K BeadChip Data Processing Using Subset Quantile Normalization for Accurate DNA Methylation Estimation

We developed a complete preprocessing pipeline for 450K BeadChip data using an original subset quantile normalization approach that performs both sample normalization and efficient Infinium I/II shift correction. The scripts, being freely available from the authors, will allow researchers to concentrate on the biological analysis of data, such as the identification of DNA methylation signatures.