Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

• DOI: 10.1093/bioinformatics/btw691
• Publication Date: 2016-11-04T12:07:31Z
• Authors: Jean-Philippe Fortin; Timothy J. Triche; Kasper D Hansen
• Keywords: Bioconductor; Normalization; R package

The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the required support HumanMethylationEPIC ('EPIC') from Illumina. We discuss methods joint analysis and normalization of data HumanMethylation450 ('450k') EPIC platforms. introduce single-sample Noob ( ssNoob ) method, a procedure suitable incremental preprocessing individual arrays conclude that this method should be when integrating multiple generations Infinium arrays. show how use reference 450k datasets estimate cell type composition samples on cumulative effect these updates ensure provides tools best integrate existing forthcoming data.The version 1.19.12 or higher available all platforms Bioconductor [e-mail] are at Bioinformatics online.