Beadarray pipeline

Beadarray specifications

Information


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
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Mark Dunning <>

Beadarray IN pipelines

 (18)
2017
PMCID: 5435826
PMID: 28573109
DOI: 10.3389/fcimb.2017.00193

[…] inc., san diego, ca) as per the manufacturer's protocol (illumina, 2010). disease and control samples were randomized between the three beadchips used. fluorescence intensities were imaged with the beadarray reader (illumina inc.). each beadchip contained 47,231 probes covering the whole-genome and known splice variants. the definition of a probe in the illumina ht-12 v4 beadchip is a 50-mer […]

2017
PMCID: 5610037
PMID: 28942197
DOI: 10.1016/j.redox.2017.09.006

[…] the beadchips were washed and stained using streptavidin-cy3 (sigma-aldrich, dorset, uk), according to manufacturer's instructions. after staining, the beadchips were scanned on an illumina beadarray reader with bead scan software (illumina)., following the beadchip scan, genomestudio software (illumina) was used to produce bead summary data from the raw data, which was exported […]

2016
PMCID: 4896498
PMID: 27272489
DOI: 10.1371/journal.pone.0156594

[…] gene expression data available at bl and fu were kept for further analysis., illumina genomestudio built-in function for detecting expressed probes was compared with the corresponding function from beadarray r package [19]. both methods use negative control probes to consider background noise. because beadarray method detect was more robust to outliers of the intensity distribution of negative […]

2016
PMCID: 4896498
PMID: 27272489
DOI: 10.1371/journal.pone.0156594

[…] function for detecting expressed probes was compared with the corresponding function from beadarray r package [19]. both methods use negative control probes to consider background noise. because beadarray method detect was more robust to outliers of the intensity distribution of negative controls, it was used for expression detection calling. each probe with a detection above background […]

2016
PMCID: 4896498
PMID: 27272489
DOI: 10.1371/journal.pone.0156594

[…] probes. for further analyses, 20,399 probes were kept which were called expressed in > 10% of all bl and > 10% of all fu samples. expression values for all samples were summarized using beadarray summarize function, log2 transformed and transformed into objects accessible by r/bioconductor package lumi [21]., distributions and variance of overall gene expression were evaluated […]

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