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

By Jean-Philippe Fortin, Timothy Triche, Kasper D. Hansen. bioRxiv, 2016

764 citations recorded by the source corpus.

The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC (”EPIC”) array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 (”450k”) and EPIC platforms. We also introduce the single-sample Noob (ssNoob) method, a normalization procedure suitable for incremental preprocessing of individual Human-Methylation arrays. Our results recommend the ssNoob method when integrating data from multiple generations of Infinium methylation arrays. Finally, we show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d670ea632b15178ecdc53a72335859a7e201067b

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Citations in the corpus

Reprogramming to recover youthful epigenetic information and restore vision (2020, positive): ““Noob” normalization was implemented using the “minfi” R package 55,56 .”
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions (2018, methodology): “This was used for TCGA data preprocessing (2) and incorporated into methylumi (12), and later also adopted by minfi (14).”