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Genome Biol. 2012 Jun 15;13(6):R44. doi: 10.1186/gb-2012-13-6-r44.

SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.

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  • 1Murdoch Childrens Research Institute, Parkville, Australia.

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.

PMID:
22703947
[PubMed - indexed for MEDLINE]
PMCID:
PMC3446316
Free PMC Article

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