Package: arrayQualityMetrics 3.69.1

Hugo Gruson

arrayQualityMetrics: Quality metrics report for microarray data sets

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

Authors:Audrey Kauffmann [aut], Wolfgang Huber [aut], Hugo Gruson [cre]

arrayQualityMetrics_3.69.1.tar.gz
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arrayQualityMetrics_3.69.1.tgz(r-4.6-any)arrayQualityMetrics_3.69.1.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
arrayQualityMetrics/json (API)

# Install 'arrayQualityMetrics' in R:
install.packages('arrayQualityMetrics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/huber-group-embl/arrayqualitymetrics/issues

On BioConductor:arrayQualityMetrics-3.69.1(bioc 3.24)arrayQualityMetrics-3.68.0(bioc 3.23)

microarrayqualitycontrolonechanneltwochannelreportwritingbioconductor

8.09 score 1 stars 337 scripts 1.0k downloads 190 mentions 19 exports 115 dependencies

Last updated from:282fcaa83d. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

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bioc-checksERROR219
linux-devel-x86_64NOTE433
source / vignettesOK623
linux-release-x86_64NOTE338
macos-release-arm64NOTE208
macos-oldrel-arm64NOTE222
windows-develNOTE256
windows-releaseNOTE227
windows-oldrelNOTE219
wasm-releaseOK161

Exports:addXYfromGALaqm.boxplotaqm.densityaqm.heatmapaqm.maplotaqm.meansdaqm.nuseaqm.pcaaqm.pmmmaqm.probesmapaqm.rleaqm.rnadegaqm.spatialaqm.writereportarrayQualityMetricsboxplotOutliersoutliersprepaffyprepdata

Dependencies:affyaffyioaffyPLMannotateAnnotationDbiaskpassbackportsbase64encbeadarrayBeadDataPackRBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbslibcachemcheckmatecliclustercolorspacecpp11crayoncurldata.tableDBIdeldirdigestevaluatefarverfastmapfontawesomeforeignFormulafsgcrmagenefiltergenericsGenomicRangesggplot2gluegridExtragridSVGgtablehexbinhighrHmischtmlTablehtmltoolshtmlwidgetshttrhwriterinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglatticelatticeExtralifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigplyrpngpreprocessCoreR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrpartRSQLiterstudioapiS4VectorsS7sassscalesSeqinfosetRNGstatmodstringistringrsurvivalsvglitesyssystemfontstextshapingtinytexvctrsviridisLitevsnwithrxfunXMLxtableXVectoryaml

Introduction: microarray quality assessment with arrayQualityMetrics
Introduction | Basic use | Affymetrix data - before preprocessing | Affymetrix data - after preprocessing | ExpressionSet and ExpressionSetIllumina | Two colour arrays, NChannelSet, RGList, MAList | Loading data from ArrayExpress | Making the report more informative by adding a factor of interest | Extended use | Spatial layout of the array | Mapping of the reporters | RNA quality | Session Info | References
Rendered fromarrayQualityMetrics.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2026-03-25

Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output
Introduction | Data preparation | Module generating functions | Outlier detection | Rendering the report | Session Info
Rendered fromaqm.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2026-03-25

Readme and manuals

Help Manual

Help pageTopics
Computing the coordinates of the spots on a slideaddXYfromGAL addXYfromGAL-methods
Write a quality reportaqm.writereport
Class to contain all the information to render a quality report module.aqmReportModule aqmReportModule-class class:aqmReportModule
Quality metrics for microarray experimentsarrayQualityMetrics
Functions for computing quality report modules.aqm.boxplot aqm.density aqm.heatmap aqm.maplot aqm.meansd aqm.nuse aqm.pca aqm.pmmm aqm.probesmap aqm.rle aqm.rnadeg aqm.spatial
Represents the results from applying an outlier detection criterion to the arrays.class:outlierDetection outlierDetection outlierDetection-class
Helper functions for outlier detection and reporting in arrayQualityMetricsboxplotOutliers outliers
Compute useful summary statistics from a data object.prepaffy prepdata