Functional normalization of 450k methylation array data improves replication in large cancer studies.
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ABSTRACT:
SUBMITTER: Fortin JP
PROVIDER: S-EPMC4283580 | biostudies-literature | 2014 Dec
REPOSITORIES: biostudies-literature
Publications
Functional normalization of 450k methylation array data improves replication in large cancer studies.
Fortin Jean-Philippe JP Labbe Aurélie A Lemire Mathieu M Zanke Brent W BW Hudson Thomas J TJ Fertig Elana J EJ Greenwood Celia Mt CM Hansen Kasper D KD
Genome biology 20141203 12
We propose an extension to quantile normalization that removes unwanted technical variation using control probes. We adapt our algorithm, functional normalization, to the Illumina 450k methylation array and address the open problem of normalizing methylation data with global epigenetic changes, such as human cancers. Using data sets from The Cancer Genome Atlas and a large case-control study, we show that our algorithm outperforms all existing normalization methods with respect to replication of ...[more]
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