ChAMP: 450k Chip Analysis Methylation Pipeline

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 normal...

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Bibliographic Details
Published in:Bioinformatics Vol. 30; no. 3; pp. 428 - 430
Main Authors: Morris, Tiffany J., Butcher, Lee M., Feber, Andrew, Teschendorff, Andrew E., Chakravarthy, Ankur R., Wojdacz, Tomasz K., Beck, Stephan
Format: Journal Article
Language:English
Published: England Oxford University Press 01.02.2014
Subjects:
Applications Notes
DNA Copy Number Variations
DNA Methylation
Oligonucleotide Array Sequence Analysis - methods
Software
ISSN:1367-4803, 1367-4811, 1367-4811, 1460-2059
Online Access:Get full text
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Summary: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 Contact:  tiffany.morris@ucl.ac.uk
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Associate Editor: John Hancock
ISSN:1367-4803
1367-4811
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btt684