ChAMP: 450k Chip Analysis Methylation Pipeline
Tiffany Morris(Genomics (United Kingdom)), Lee M Butcher(Genomics (United Kingdom)), Andrew Feber(Genomics (United Kingdom)), Andrew E. Teschendorff(Genomics (United Kingdom)), Ankur Chakravarthy(Genomics (United Kingdom)), Tomasz K. Wojdacz(Genomics (United Kingdom)), Stephan Beck(Genomics (United Kingdom))
Cited by 1,140Open Access
Abstract
UNLABELLED: 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 bioconductor.org
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