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Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip

Bioconductor version: 3.1

Illumina HumanMethylation450 BeadChip has a complex array design, and the measurement is subject to experimental variations. The ENmix R package provides tools for low level data preprocessing to improve data quality. It incorporates a model based background correction method ENmix, and provides functions for inter-array quantile normalization, data quality checking, exploration of multimodally distributed CpGs and source of data variation. To support large scale data analysis, the package also provides multi-processor parallel computing wrappers for some commonly used data preprocessing methods, such as BMIQ probe design type bias correction and ComBat batch effect correction.

Author: Zongli Xu [cre, aut], Liang Niu [aut], Leping Li [ctb], Jack Taylor [ctb]

Maintainer: Zongli Xu <xuz at>

Citation (from within R, enter citation("ENmix")):


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PDF R Script ENmix User's Guide
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, DNAMethylation, DataImport, MethylationArray, Microarray, Normalization, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 1.0.0
In Bioconductor since BioC 3.1 (R-3.2) (< 6 months)
License Artistic-2.0
Depends minfi, parallel, doParallel, Biobase(>= 2.17.8), foreach
Imports MASS, preprocessCore, wateRmelon, sva, geneplotter
Suggests minfiData(>= 0.4.1), RPMM, RUnit, BiocGenerics
Depends On Me
Imports Me
Suggests Me
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