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Analysing Illumina HumanMethylation BeadChip Data

Bioconductor version: Release (3.19)

Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

Author: Belinda Phipson and Jovana Maksimovic

Maintainer: Belinda Phipson <phipson.b at>, Jovana Maksimovic <jovana.maksimovic at>, Andrew Lonsdale <andrew.lonsdale at>

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


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:

missMethyl: Analysing Illumina HumanMethylation BeadChip Data HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, GeneSetEnrichment, GeneticVariability, GenomicVariation, MethylationArray, Normalization, Software
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License GPL-2
Depends R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Imports AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi,, ruv, S4Vectors, statmod, stringr, SummarizedExperiment
System Requirements
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Suggests BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub
Linking To
Depends On Me methylationArrayAnalysis
Imports Me DMRcate, MEAL, methylGSA
Suggests Me RnBeads
Links To Me
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Source Package missMethyl_1.38.0.tar.gz
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macOS Binary (x86_64) missMethyl_1.38.0.tgz
macOS Binary (arm64) missMethyl_1.38.0.tgz
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