Review of processing and analysis methods for DNA methylation array data Public Deposited

http://ir.library.oregonstate.edu/concern/articles/t435gk15n

This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the Nature Publishing Group and can be found at:  http://www.nature.com/bjc/index.html.

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  • The promise of epigenome-wide association studies (EWAS) and cancer specific somatic 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, as well as to summarize advantages of recent approaches proposed for handling those issues; focusing on approaches publicly available in open-source environments such as R and Bioconductor. The processing tools and analysis flowchart described we hope will facilitate researchers to effectively use these powerful DNA methylation array-based platforms, thereby advancing our understanding of human health and disease.
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  • Wilhelm-Benartzi, C. S., Koestler, D. C., Karagas, M. R., Flanagan, J. M., Christensen, B. C., Kelsey, K. T., . . . Brown, R. (2013). Review of processing and analysis methods for DNA methylation array data. British Journal of Cancer, 109(6), 1394-1402. doi:10.1038/bjc.2013.496
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