Functional normalization of 450k methylation array data improves replication in large cancer studies

@inproceedings{Fortin2014FunctionalNO,
  title={Functional normalization of 450k methylation array data improves replication in large cancer studies},
  author={Jean-Philippe Fortin and Aur{\'e}lie Labbe and Mathieu Lemire and Brent W. Zanke and Thomas J. Hudson and Elana J. Fertig and Celia M T Greenwood and Kasper D. Hansen},
  booktitle={Genome Biology},
  year={2014}
}
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… CONTINUE READING
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shinyMethyl : interactive quality control of Illumina 450 kDNAmethylation arrays in R

  • BR Joubert, SE Håberg, +13 authors SJ London
  • F 1000 Research
  • 2014

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