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ChAMP: 450k Chip Analysis Methylation Pipeline.

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

SUBMITTER: Morris TJ 

PROVIDER: S-EPMC3904520 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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ChAMP: 450k Chip Analysis Methylation Pipeline.

Morris Tiffany J TJ   Butcher Lee M LM   Feber Andrew A   Teschendorff Andrew E AE   Chakravarthy Ankur R AR   Wojdacz Tomasz K TK   Beck Stephan S  

Bioinformatics (Oxford, England) 20131212 3

<h4>Unlabelled</h4>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.<h4>Availability and implementation</h4>ChAMP  ...[more]

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