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arrayQualityMetrics specifications


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
Version 3.36.0
Stability Stable
limma, methods, stats, RColorBrewer, grid, graphics, Biobase, utils, BiocStyle, grDevices, lattice, affy, knitr, genefilter, beadarray, latticeExtra, Hmisc, hwriter, XML, affyPLM(>=1.27.3), Cairo(>=1.4-6), gridSVG(>=1.4-3), setRNG, vsn(>=3.23.3), ALLMLL, CCl4
Maintained Yes


No version available


Publications for arrayQualityMetrics

arrayQualityMetrics citations


Specific Transcriptome Changes Associated with Blood Pressure Reduction in Hypertensive Patients After Relaxation Response Training

PMCID: 5961875
PMID: 29616846
DOI: 10.1089/acm.2017.0053

[…] phate dehydrogenase) as well as spike-in control transcripts. Reproducibility of the samples was checked by using chip-to-chip correlation and signal-to-noise ratio methods for replicate arrays using arrayQualityMetrics, a Bioconductor package in R. Based on these quality control analyses, microarrays for two pairs of pre- and post-RR patients (one responder and one nonresponder) were excluded fro […]


In vitro RNA seq based toxicogenomics assessment shows reduced biological effect of tobacco heating products when compared to cigarette smoke

Sci Rep
PMCID: 5799303
PMID: 29402904
DOI: 10.1038/s41598-018-19627-0

[…] otine, functional endpoints/immunohistochemistry and cytokines, an unpaired t-test was used to perform comparisons of treatments versus air control.For the RNA-seq, samples were QC analyzed using the arrayQualityMetrics package in Bioconductor. Outliers were identified based on 4 parameters, maplot, boxplot, heatmap and manual inspection. The RNAseq data was preprocessed and aligned to the human g […]


The Immunome in Two Inherited Forms of Pulmonary Fibrosis

Front Immunol
PMCID: 5797737
PMID: 29445374
DOI: 10.3389/fimmu.2018.00076

[…] ly, Affymetrix CEL files were processed with Affymetrix Power Tools for probeset summarization, normalization and log2-transformation (RMA with sketch quantile normalization). Quality assessment with arrayQualityMetrics R package detected no outlying arrays. Probesets (1) not annotated with any gene symbol, (2) associated with multiple gene symbols, and (3) having very low variability (with interq […]


Effects of anti‐inflammatory drugs on the expression of tryptophan‐metabolism genes by human macrophages

PMCID: 5918594
PMID: 29377288
DOI: 10.1002/JLB.3A0617-261R

[…] Analysis was performed using R/Bioconductor packages “arrayQualityMetrics,” “oligo,” and “nlme.” Normalization was performed using RMA. Probesets were collapsed down to a single gene. These data are available on Gene Expression Omnibus (GEO GSE85333).Dif […]


Cattle infection response network and its functional modules

BMC Immunol
PMCID: 5755453
PMID: 29301495
DOI: 10.1186/s12865-017-0238-4

[…] nalysis algorithm (RMA) for background adjustment with quantile normalization as implemented in the R affy package []. Quality tests were performed on the normalized array data using the Bioconductor arrayQualityMetrics package []. Arrays that failed all three outlier tests (i.e. Distances between arrays, Boxplots and MA plots) were excluded from further analyses. The final data set contained a to […]


Mesenchyme derived factors enhance preneoplastic growth by non genotoxic carcinogens in rat liver

PMCID: 5818586
PMID: 29270806
DOI: 10.1007/s00204-017-2080-0
call_split See protocol

[…] EL files) into the R programming language and environment for statistical computing, sufficient quality of the raw data was checked by various metrics and statistical analyses provided by the package ArrayQualityMetrics (Kauffmann et al. ). With the help of the RMA method data were normalized and probesets were mapped to gene symbols and Entrez IDs using the appropriate metadata packages of Biocon […]


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

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