DOI: 10.18129/B9.bioc.MethylAid    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MethylAid.

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Bioconductor version: 3.8

A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Author: Maarten van Iterson [aut, cre], Elmar Tobi[ctb], Roderick Slieker[ctb], Wouter den Hollander[ctb], Rene Luijk[ctb] and Bas Heijmans[ctb]

Maintainer: M. van Iterson <mviterson at>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


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



PDF R Script MethylAid: Visual and Interactive quality control of Illumina Human DNA Methylation array data
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization
Version 1.16.0
In Bioconductor since BioC 3.0 (R-3.1) (4.5 years)
License GPL (>= 2)
Depends R (>= 3.4)
Imports Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi(>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils
Suggests BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit
Depends On Me MethylAidData
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MethylAid_1.16.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) MethylAid_1.16.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

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