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Br J Cancer. 2013 Sep 17;109(6):1394-402. doi: 10.1038/bjc.2013.496. Epub 2013 Aug 27.

Review of processing and analysis methods for DNA methylation array data.

Author information

1
Epigenetics Unit, Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Ovarian Cancer Action Research Centre, Imperial College London, 4th floor IRDB, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.

Abstract

The promise of epigenome-wide association studies and cancer-specific somatic DNA methylation changes in improving our understanding of cancer, coupled with the decreasing cost and increasing coverage of DNA methylation microarrays, has brought about a surge in the use of these technologies. Here, we aim to provide both a review of issues encountered in the processing and analysis of array-based DNA methylation data and a summary of the advantages of recent approaches proposed for handling those issues, focusing on approaches publicly available in open-source environments such as R and Bioconductor. We hope that the processing tools and analysis flowchart described herein will facilitate researchers to effectively use these powerful DNA methylation array-based platforms, thereby advancing our understanding of human health and disease.

PMID:
23982603
PMCID:
PMC3777004
DOI:
10.1038/bjc.2013.496
[Indexed for MEDLINE]
Free PMC Article

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