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This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see ENmix.

Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip

Bioconductor version: 3.2

Illumina HumanMethylation450 BeadChip array measurements have intrinsic levels of background noise that degrade methylation measurement. The ENmix package provides an efficient data pre-processing tool designed to reduce background noise and improve signal for DNA methylation estimation. The package utilizes a novel model-based background correction method, ENmix, that significantly improve accuracy and reproducibility of methylation measures. The data structure used by the ENmix package is compatible with several other related R packages, such as minfi, wateRmelon and ChAMP, providing straightforward integration of ENmix-corrected datasets for subsequent data analysis. The software is designed to support large scale data analysis, and provides multi-processor parallel computing wrappers for commonly used data preprocessing methods, including BMIQ probe design type bias correction and ComBat batch effect correction. In addition ENmix package has selectable complementary functions for efficient data visualization (such as data distribution plotting), quality control (identification and filtering of low quality data points, samples, probes, and outliers, along with imputation of missing values), inter-array normalization (3 different quantile normalizations), identification of probes with multimodal distributions due to SNPs and other factors, and exploration of data variance structure using principal component regression analysis plots. Together these provide a set of flexible and transparent tools for preprocessing of EWAS data in a computationally-efficient and user-friendly package.

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

Maintainer: Zongli Xu <xuz at>

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PDF ENmix User's Guide
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, DNAMethylation, DataImport, MethylationArray, Microarray, Normalization, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 1.4.1
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License Artistic-2.0
Depends minfi, parallel, doParallel, Biobase(>= 2.17.8), foreach
Imports MASS, preprocessCore, wateRmelon, sva, geneplotter, impute
Suggests minfiData(>= 0.4.1), RPMM, RUnit, BiocGenerics
Depends On Me
Imports Me
Suggests Me
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