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beadarraySNP specifications


Unique identifier OMICS_02056
Name beadarraySNP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.49.0
Stability Stable
methods, Biobase, quantsmooth
Maintained Yes




No version available



  • person_outline Jan Oosting

beadarraySNP citations


Loss of Heterozygosity and Copy Number Alterations in Flow Sorted Bulky Cervical Cancer

PLoS One
PMCID: 3706587
PMID: 23874418
DOI: 10.1371/journal.pone.0067414

[…] y. The samples were genotyped in Illumina Beadstudio 2.3. The reference genotype clusters were derived from the normal samples in the dataset, and genotypes and allele intensities were extracted. The beadarraySNP package was used for further data processing. The analysis steps are depicted in . SNPs that deviated significantly from Hardy-Weinberg equilibrium (at a significance level of 0.05, divid […]


Data analysis issues for allele specific expression using Illumina's GoldenGate assay

BMC Bioinformatics
PMCID: 2887809
PMID: 20504309
DOI: 10.1186/1471-2105-11-280

[…] ta, the summary log2(Cy3) and log2(Cy5) values from each array were quantile normalized (within-array) and log-ratios were calculated. This analysis was carried out in R [] using the beadarray [] and beadarraySNP packages.BeadStudio output from the dye-swap experiment in Tan et al. (2008) was provided by Aik Choon Tan (personal communication). For each array, log-ratios and average log-intensities […]


R/Bioconductor software for Illumina's Infinium whole genome genotyping BeadChips

PMCID: 2752620
PMID: 19661241
DOI: 10.1093/bioinformatics/btp470

[…] noulatou et al., ; Teo et al., ) including Illumina's GenCall algorithm in BeadStudio/GenomeStudio are also available. Software for the analysis of Illumina data such as beadarray (Dunning et al., ), beadarraySNP and lumi (Du et al., ) is available in R/Bioconductor (Gentleman et al., ); however, current packages do not deal specifically with Infinium BeadChip data.In this article, we present the […]


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