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

Bioconductor version: Release (3.19)

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: L.J.Sinke <L.J.Sinke at>

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


To install this package, start R (version "4.4") and enter:

if (!require("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:

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


biocViews BatchEffect, DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (10 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
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Suggests BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit
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Depends On Me MethylAidData
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Source Package MethylAid_1.38.0.tar.gz
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