Journal article
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.
J Maksimovic, L Gordon, A Oshlack
Genome Biology | BMC | Published : 2012
Open access
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.
Grants
Funding Acknowledgements
We thank Kasper Hansen, Martin Aryee and Rafael Irizarry for making their minfi code available and including our methods. We thank Mark Robinson for helpful discussion and critical reading of the manuscript. We also acknowledge Terry Speed, Nadia Davidson, the Cancer and Disease Epigenetics (Saffery) Lab and Early Life Epigenetics (Craig) Lab at the Murdoch Childrens Research Institute (MCRI) for helpful discussion. We thank David Martino and Marina Bibikova for providing access to their published data. We would also like to acknowledge the TCGA Research Network for making their vast resource of genomic data available. This work was supported by the Victorian Government's Operational Infrastructure Support Program to MCRI.