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Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: Release (3.1)

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 <Mark.Dunning at>

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


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


biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software
Version 2.18.0
In Bioconductor since BioC 1.8 (R-2.3) (9.5 years)
License GPL-2
Depends R (>= 2.13.0), BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), methods, ggplot2
Imports BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio
Suggests lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
Depends On Me beadarrayExampleData
Imports Me arrayQualityMetrics, BeadArrayUseCases, blima, epigenomix
Suggests Me beadarraySNP, blimaTestingData, lumi
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