DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging

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 t...

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Detalles Bibliográficos
Autores principales: Phipson, Belinda, Oshlack, Alicia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210618/
https://www.ncbi.nlm.nih.gov/pubmed/25245051
http://dx.doi.org/10.1186/s13059-014-0465-4
Descripción
Sumario: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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0465-4) contains supplementary material, which is available to authorized users.

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