ChAMP: 450k Chip Analysis Methylation Pipeline

Bioinformatics. 2014 Feb 1;30(3):428-30. doi: 10.1093/bioinformatics/btt684. Epub 2013 Dec 12.


The Illumina Infinium HumanMethylation450 BeadChip is a new platform for high-throughput DNA methylation analysis. Several methods for normalization and processing of these data have been published recently. Here we present an integrated analysis pipeline offering a choice of the most popular normalization methods while also introducing new methods for calling differentially methylated regions and detecting copy number aberrations.

Availability and implementation: ChAMP is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Copy Number Variations
  • DNA Methylation*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Software*