arrayQualityMetrics specifications

Information


Unique identifier OMICS_02005
Name arrayQualityMetrics
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


arrayQualityMetrics article

arrayQualityMetrics citations

 (3)
2017
PMCID: 5537386

[…] r/bioconductor package complexheatmap [9]. intensities are row-normalized between 0 and 1 (fig. 3, fig. 4). fig. 4 additionally includes color-coded fold changes. we used the r/bioconductor package arrayqualitymetrics [10] to validate the quality of the microarray experiment (supplementary material 2)., , , , this work was supported by intramural funds and by the foundation klaus […]

2014
PMCID: 4115254

[…] usa) following the manufacturer’s instructions., microarray data were analysed using r (r development core team, 2010) and bioconductor tools (gentleman et al., 2004). after quality control with the arrayqualitymetrics package (kauffmann et al., 2009), expression intensities were normalized with rma function with the oligo package (carvalho and irizarry, 2010). genes differentially expressed […]

2013
PMCID: 3857903

[…] (available at http://bioconductor.org/, [20]). raw data from microarray experiments were obtained from the geo repository (http://www.ncbi.nlm.nih.gov/geo/, [21]) and were examined using the arrayqualitymetrics package, followed by normalization and nonspecific filtering with affyplm and genefilter packages, where necessary. ultimately, 12,177 genes with expression values measured for 19 […]

arrayQualityMetrics institution(s)
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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