Online

A package that provides a background correction method which uses a mixture of exponential and truncated normal distributions to flexibly model signal intensity and uses a truncated normal distribution to model background noise. Depending on data availability, three approaches are employed to estimate background normal distribution parameters using (i) internal chip negative controls, (ii) out-of-band Infinium I probe intensities or (iii) combined methylated and unmethylated intensities. Evaluation results in both duplicates and experimental standard samples showed that ENmix outperformed commonly used background subtraction methods in terms of improvement in replicability and accuracy as well as reducing probe design bias. After ENmix background correction the resulting data can be used with other commonly-used preprocessing methods including quantile normalization for between-sample normalization and BMIQ for further correction of probe-design bias.

User report

0 user reviews

0 user reviews

No review has been posted.

ENmix forum

No open topic.

ENmix versioning

No versioning.

ENmix classification

ENmix specifications

Software type:
Package
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
ENmix version 1.0.0
Requirements:
minfi, parallel, doParallel, Biobase(>= 2.17.8), foreach
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable

Publications

  • (Xu et al., 2015) ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic acids research.
    PMID: 26384415
  • (Pidsley et al., 2013) A data-driven approach to preprocessing Illumina 450K methylation array data. BMC genomics.
    PMID: 23631413
  • (Teschendorff et al., 2013) A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics.
    PMID: 23175756
  • (Niu et al., 2016) RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics.
    PMID: 27153672
  • (Xu et al., 2017) RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip. BMC Genomics.
    DOI: 10.1186/s12864-016-3426-3

ENmix support

Maintainer

Credits

Institution(s)

Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA

Funding source(s)

Intramural Research Program of the NIH, National Institute of Environmental Health Sciences [Z01 ES044005, Z01 ES101765, Z01 ES049033, Z01 ES049032]

Link to literature

Related DNA methylation array analysis tools

Most Recent Tools

methylSpectrum
Desktop

methylSpectrum

Deconvolutes of DNA methylation array data into source contributions from…

Deconvolutes of DNA methylation array data into source contributions from distinct cell types. methylSpectrum is a method for inferring changes in the distribution of white blood cells between…

DiMmeR
Desktop

DiMmeR Discovery of Multiple Differentially Methylated Regions

Guides scientists the whole way through EWAS data analysis. DiMmer offers…

Guides scientists the whole way through EWAS data analysis. DiMmer offers parallelized statistical methods for identifying DMRs in both Illumina 450K and 850K EPIC chip data and also methylated…

PyMAP
Desktop

PyMAP

A native python module for analysis of 450k methylation platform. PyMAP can be…

A native python module for analysis of 450k methylation platform. PyMAP can be easily deployed to cloud platforms that support python scripting language for large-scale methylation studies. By…

ICDMR
Desktop

ICDMR Identification of Consistently Differentially Methylated Regions

Analyzes methylation intensity data generated from tiling arrays to locate DMRs…

Analyzes methylation intensity data generated from tiling arrays to locate DMRs across a large set of samples simultaneously. ICDMR provides a way to calculate the concordance between adjacent…

Most Popular Tools

FastDMA
Desktop

FastDMA

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which…

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.

16 related tools

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.