Phipson B, Oshlack A. DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging.
Genome Biol 2014;
15:465. [PMID:
25245051 PMCID:
PMC4210618 DOI:
10.1186/s13059-014-0465-4]
[Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 09/10/2014] [Indexed: 01/17/2023] Open
Abstract
Methylation of DNA is known to be essential to development and dramatically altered in cancers. The Illumina HumanMethylation450 BeadChip has been used extensively as a cost-effective way to profile nearly half a million CpG sites across the human genome. Here we present DiffVar, a novel method to test for differential variability between sample groups. DiffVar employs an empirical Bayes model framework that can take into account any experimental design and is robust to outliers. We applied DiffVar to several datasets from The Cancer Genome Atlas, as well as an aging dataset. DiffVar is available in the missMethyl Bioconductor R package.
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