arrayQualityMetrics protocols

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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


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Publication for arrayQualityMetrics

arrayQualityMetrics in pipelines

PMCID: 5339674
PMID: 28202494
DOI: 10.1084/jem.20161087

[…] in the arrayexpress database under accession no. e-mtab-5425., for bioinformatics analyses, a total of seven arrays (n = 3 fh1fl/fl; n = 4 fh1fl/fl;vav-icre) were quality control analyzed using the arrayqualitymetrics package in bioconductor. normalization of the 29,638 features across all arrays was achieved using the robust multiarray average expression measure. pairwise group comparisons […]

PMCID: 5352142
PMID: 28248954
DOI: 10.1371/journal.pgen.1006643

[…] was generated using humanht-12v4 beadchips (illumina), according to the standard protocol. preprocessing and quality control of the data was done using r [] and the bioconductor packages lumi [] and arrayqualitymetrics []. the number of samples retained for further analysis was 293 for cd4+ and 283 for cd8+ t cells, 303 unique individuals. the effect of the mutant and wild-type il27 […]

PMCID: 5397247
PMID: 28406754
DOI: 10.1089/ten.tec.2016.0329

[…] were converted into text files for analysis. probe sample profiles and control profiles were uploaded into the statistical programming language r (version 3.1.2). bioconductor packages lumi and arrayqualitymetrics software packages were used for quality control. all measured samples passed quality control. data were further processed using the bioconductor package limma., output values […]

PMCID: 5443531
PMID: 28542390
DOI: 10.1371/journal.pone.0178151

[…] cy3, and scanned in the illumina iscan reader, with output produced by genomestudio version 1.9.0. using r (version 3.1.2) []. the data underwent quality control through the bioconductor [] packages arrayqualitymetrics [], made4 [], lumi [] and limma []. the detectable probe ratio of each probe was calculated, and all probes with a detection p-value of less than 0.01 were removed, and relative […]

PMCID: 5464771
PMID: 28594327
DOI: 10.7554/eLife.23190.030

[…] source software r (version 3.1.0, using packages from bioconductor ( cel files with raw data were used and the quality control analysis was performed using arrayqualitymetrics package (). the raw data were preprocessed using the rma method available in the oligo package (). probes with no annotation were removed from analysis. finally, the resulting […]

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arrayQualityMetrics in publications

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

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

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

[…] 500 ng of rna was prepared using standard affymetrix protocols and applied to the human gene 2.1 st array by edinburgh genomics (edinburgh, uk)., 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)., d […]

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

[…] 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 […]

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

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