Registration Open for Bioc2024 July 24-26


Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: Release (3.19)

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Author: Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie

Maintainer: Mark Dunning <m.j.dunning at>

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


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:

beadarray.pdf PDF R Script
beadlevel.pdf PDF R Script
beadsummary.pdf PDF R Script
ImageProcessing.pdf PDF R Script
Reference Manual PDF


biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software
Version 2.54.0
In Bioconductor since BioC 1.8 (R-2.3) (18 years)
License MIT + file LICENSE
Depends R (>= 2.13.0), BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), hexbin
Imports BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2
System Requirements
See More
Suggests lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
Linking To
Depends On Me beadarrayExampleData
Imports Me arrayQualityMetrics, blima, epigenomix, BeadArrayUseCases, RobLoxBioC
Suggests Me lumi, blimaTestingData, maGUI
Links To Me
Build Report Build Report

Package Archives

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

Source Package beadarray_2.54.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) beadarray_2.54.0.tgz
macOS Binary (arm64) beadarray_2.54.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats