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
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author Phipson, Belinda
Oshlack, Alicia
author_facet Phipson, Belinda
Oshlack, Alicia
author_sort Phipson, Belinda
collection PubMed
description 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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spelling pubmed-42106182014-10-29 DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging Phipson, Belinda Oshlack, Alicia Genome Biol Method 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. BioMed Central 2014-09-23 2014 /pmc/articles/PMC4210618/ /pubmed/25245051 http://dx.doi.org/10.1186/s13059-014-0465-4 Text en © Phipson and Oshlack; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Phipson, Belinda
Oshlack, Alicia
DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
title DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
title_full DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
title_fullStr DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
title_full_unstemmed DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
title_short DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
title_sort diffvar: a new method for detecting differential variability with application to methylation in cancer and aging
topic Method
url 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
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