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This is the development version of MethylAid; for the stable release version, see MethylAid.

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

Bioconductor version: Development (3.5)

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>

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


biocViews BatchEffect, DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization
Version 1.9.0
In Bioconductor since BioC 3.0 (R-3.1) (2 years)
License GPL (>= 2)
Depends R (>= 3.0)
Imports Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi(>= 1.17.9), methods, RColorBrewer, shiny, stats, utils
Suggests BiocStyle, knitr, MethylAidData, minfiData, RUnit
Depends On Me
Imports Me
Suggests Me
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