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

被引：567

作者：

Fortin, Jean-Philippe ^{[1
]}

Triche, Timothy J., Jr. ^{[2
]}

Hansen, Kasper D. ^{[1
,3
]}

机构：

[1] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD 21205 USA

[2] USC, Keck Sch Med, Jane Anne Nohl Div Hematol, Los Angeles, CA 90033 USA

[3] Johns Hopkins Sch Med, McKusick Nathans Inst Genet Med, Baltimore, MD 21205 USA

来源：

BIOINFORMATICS | 2017年 / 33卷 / 04期

基金：

美国国家卫生研究院;

关键词：

DNA METHYLATION; CELLULAR HETEROGENEITY; BIOCONDUCTOR;

D O I：

10.1093/bioinformatics/btw691

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 introduce the single-sample Noob (ssNoob) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. 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 Illuminamethylation array data.

引用

页码：558 / 560

页数：3

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