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Open Access Method

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

Jovana Maksimovic, Lavinia Gordon and Alicia Oshlack*

Author affiliations

Murdoch Childrens Research Institute, 50 Flemington Road, Parkville 3052, Australia

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Citation and License

Genome Biology 2012, 13:R44  doi:10.1186/gb-2012-13-6-r44

Published: 15 June 2012

Abstract

DNA methylation is the most widely studied epigenetic mark and is known to be essential to normal development and frequently disrupted in disease. The Illumina HumanMethylation450 BeadChip assays the methylation status of CpGs at 485,577 sites across the genome. Here we present Subset-quantile Within Array Normalization (SWAN), a new method that substantially improves the results from this platform by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.