arrayQualityMetrics pipeline

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


Publication for arrayQualityMetrics

arrayQualityMetrics IN pipelines

 (6)
2017
PMCID: 5506428
PMID: 28597562
DOI: 10.1111/acel.12621

[…] each sample. gene expression data from affymetrix hugene 2.0 microarrays were normalized using the rma function of the r oligo package. quality analysis of the microarrays was performed using the r arrayqualitymetrics package. fold change and significance for transcript cluster identifiers between conditions were determined using the r limma package and annotated using […]

2017
PMCID: 5537386
PMID: 28795085
DOI: 10.1016/j.dib.2017.07.018

[…] 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 […]

2017
PMCID: 5643418
PMID: 29075261
DOI: 10.3389/fimmu.2017.01276

[…] only probes significantly detected (p < 0.05) in 60% of all samples, yielding 14,302 genes. this preprocessed dataset was used for all subsequent analyses. quality control was performed using the arrayqualitymetrics() function in r (51) and led to the exclusion of 14 samples. de genes were determined by fitting a linear regression model including post-vaccination time point and date […]

2014
PMCID: 4115254
PMID: 24477640
DOI: 10.1093/jxb/ert489

[…] 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: 3764031
PMID: 24040155
DOI: 10.1371/journal.pone.0074034

[…] az, usa). microarray data were normalized using different methods: average normalization and cyclicloess. the quality of the outcome was assessed by different plots produced by the software package arrayqualitymetrics implemented in the r language. a supervised method (significance analysis of microarrays -sam-) [17] was then used to find the more significant (adjusted p<0.05) differentially […]

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

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