SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
Murdoch Childrens Research Institute, 50 Flemington Road, Parkville 3052, Australia
Genome Biology 2012, 13:R44 doi:10.1186/gb-2012-13-6-r44Published: 15 June 2012
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.