SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.
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.
Murdoch Childrens Research Institute, Parkville, Australia.
Jovana
J
Maksimovic
Lavinia
L
Gordon
Alicia
A
Oshlack
D018899:CpG Islands; D019175:DNA Methylation; D015342:DNA Probes / Q000235:genetics; D004273:DNA, Neoplasm / Q000032:analysis / Q000235:genetics; D005260:Female; D015894:Genome, Human; D006801:Humans; D061986:MCF-7 Cells; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
D015342:DNA Probes; D004273:DNA, Neoplasm