Beadarray protocols

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Beadarray specifications


Unique identifier OMICS_02021
Name Beadarray
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.30.0
Stability Stable
AnnotationDbi, limma, methods, IRanges, GenomicRanges, BiocStyle, stats4, ggplot2, affy, knitr, reshape2, illuminaio, vsn, beadarrayExampleData, R(>=2.13.0), TxDb.Hsapiens.UCSC.hg19.knownGene, hwriter, Biobase(>=2.17.8), lumi, BiocGenerics(>=0.3.2), BeadDataPackR, illuminaHumanv3.db, gridExtra, ggbio, Nozzle.R1
Maintained Yes


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  • person_outline Mark Dunning <>

Beadarray in pipelines

PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] <character> <character> ## cg00050873 ## cg00212031 ## cg00213748 ## cg00214611 promoter_associated_cell_type_specific ## cg00455876 ## cg01707559 , as for their many other beadarray platforms, illumina methylation data is usually obtained in the form of intensity data (idat) files. this is a proprietary format that is output by the scanner and stores summary […]

PMCID: 5270243
PMID: 28128285
DOI: 10.1038/srep41483

[…] beadchip arrays (illumina). hybridized biotinylated crna was detected with 1 μg/ml cyanine3-streptavidine (amersham biosciences, pistacataway, nj, usa). beadchips were scanned with the illumina beadarray reader. the accuracy of this array has been previously tested in our tvs validation study where the results of 192 differentially expressed genes were verified by rt-pcr. the correlation […]

PMCID: 5335253
PMID: 28256545
DOI: 10.1038/srep43478

[…] and data extracted using the genomestudio software., raw, probe level summary values as exported from illumina genomestudio 2011 of illumina humanht 12 v4 microarrays were imported into r using beadarray. probes were background corrected followed by quantile normalization using the neqc command. the analysis was restricted to probes with a detection p-value of less than 0.01 in at least 10% […]

PMCID: 5362446
PMID: 28118602
DOI: 10.18632/oncotarget.14739

[…] step. samples were randomized with respect to sample type, patient age and estrogen receptor (er) status (13) across four 450k beadchips. hybridized and processed arrays were scanned using illumina beadarray reader with high-density (hd) technology and beadscan software. the raw intensity was then extracted using the genomestudio module., the raw data from genomestudio was summarized […]

PMCID: 5410301
PMID: 28423573
DOI: 10.18632/oncotarget.15574

[…] inc., san diego, ca) at 58°c overnight. array chips were washed with manufacturer's e1bc solution, stained with 1 ug/ml cy3-streptavidine (amersham biosciences) and eventually scanned with illumina beadarray reader. we collected primary data using the supplied scanner software and the following analyses were performed using the beadstudio version 3 software package. raw data was normalized […]

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Beadarray in publications

PMCID: 5954140
PMID: 29765046
DOI: 10.1038/s41467-018-04244-2

[…] used for labeling and hybridization to human beadchip v4 microarrays (illumina, san diego, ca) in accordance with the manufacturer’s protocols. after the bead chips were scanned with an illumina beadarray reader, the microarray data were normalized using the quantile normalization method in the linear models for microarray data package in the r language environment. the expression level […]

PMCID: 5940812
PMID: 29622769
DOI: 10.1038/s12276-017-0001-1

[…] diego, ca). array signals were developed by amersham fluorolink streptavidin-cy3 (ge healthcare bio-sciences, little chalfont, uk) following the beadchip manual. arrays were scanned with an illumina beadarray reader confocal scanner (beadstation 500gxdw; illumina) according to the manufacturer's instructions. array data processing and analysis used illumina beadstudio software. the beadstudio […]

PMCID: 5895731
PMID: 29675033
DOI: 10.3389/fgene.2018.00108

[…] hybridized using the whole-genome protocol from dasl ht assay (illumina, san diego, ca, united states) and ovation® ffpe wta-systems (nugen, san carlos, ca, united states) to an illumina humanref-12 beadarray (illumina, san diego, ca, united states) according to the manufacturer’s protocol. raw bead count data was analyzed using the r/bioconductor package beadarray () followed by quantile […]

PMCID: 5883342
PMID: 29614955
DOI: 10.1186/s12881-018-0563-3

[…] in our samples, the call rate for non-diploid genotypes in the 7q11.23 ws locus was 99%, which is similar to those reported for diploid calls in other regions (97.9%–99.9%) using illumina beadarray chips []. there are multiple potential sources for non-called or miscalled snps using snp-chips. as described by pompanon et al., these may include dna sample quality, interactions […]

PMCID: 5882800
PMID: 29615635
DOI: 10.1038/s41598-018-23063-5

[…] the obtained dna was treated with bisulfite and hybridized to hm450 beadarrays following the manufacturer’s guidelines. the dna was labeled with a fluorescent dye and then scanned using an illumina beadarray reader. sequencing data was analyzed using the reference sequence of the human reference genome hg18. some transcripts are presented as common synonyms identified in literature search […]

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Beadarray reviews

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