To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ENmix")

In most cases, you don't need to download the package archive at all.

ENmix

 

Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip

Bioconductor version: Release (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 niehs.nih.gov>

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

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ENmix")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ENmix")

 

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

Details

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
LinkingTo
Suggests minfiData(>= 0.4.1), RPMM, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source ENmix_1.0.0.tar.gz
Windows Binary ENmix_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) ENmix_1.0.0.tgz
Mac OS X 10.9 (Mavericks) ENmix_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ENmix/tree/release-3.1
Package Short Url http://bioconductor.org/packages/ENmix/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center