Package: arrayQualityMetrics 3.63.0
Mike Smith
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:
arrayQualityMetrics_3.63.0.tar.gz
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arrayQualityMetrics.pdf |arrayQualityMetrics.html✨
arrayQualityMetrics/json (API)
NEWS
| # Install 'arrayQualityMetrics' in R: |
| install.packages('arrayQualityMetrics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/grimbough/arrayqualitymetrics/issues
On BioConductor:arrayQualityMetrics-3.63.0(bioc 3.21)arrayQualityMetrics-3.62.0(bioc 3.20)
microarrayqualitycontrolonechanneltwochannelreportwriting
Last updated 4 months agofrom:c608533fa1. Checks:1 ERROR, 6 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | FAIL | Jan 30 2025 |
| R-4.5-win | WARNING | Jan 30 2025 |
| R-4.5-linux | WARNING | Jan 30 2025 |
| R-4.4-win | WARNING | Jan 30 2025 |
| R-4.4-mac | WARNING | Jan 30 2025 |
| R-4.3-win | WARNING | Jan 30 2025 |
| R-4.3-mac | WARNING | Jan 30 2025 |
Exports:addXYfromGALaqm.boxplotaqm.densityaqm.heatmapaqm.maplotaqm.meansdaqm.nuseaqm.pcaaqm.pmmmaqm.probesmapaqm.rleaqm.rnadegaqm.spatialaqm.writereportarrayQualityMetricsboxplotOutliersoutliersprepaffyprepdata
Dependencies:affyaffyioaffyPLMannotateAnnotationDbiaskpassbackportsbase64base64encbeadarrayBeadDataPackRBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbslibcachemcheckmatecliclustercolorspacecpp11crayoncurldata.tableDBIdeldirdigestevaluatefansifarverfastmapfontawesomeforeignFormulafsgcrmagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragridSVGgtablehexbinhighrHmischtmlTablehtmltoolshtmlwidgetshttrhwriterilluminaiointerpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglatticelatticeExtralifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngpreprocessCoreR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalessetRNGstatmodstringistringrsurvivalsvglitesyssystemfontstibbletinytexUCSC.utilsutf8vctrsviridisviridisLitevsnwithrxfunXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Computing the coordinates of the spots on a slide | addXYfromGAL addXYfromGAL-methods |
| Write a quality report | aqm.writereport |
| Class to contain all the information to render a quality report module. | aqmReportModule aqmReportModule-class class:aqmReportModule |
| Quality metrics for microarray experiments | arrayQualityMetrics |
| 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 arrayQualityMetrics | boxplotOutliers outliers |
| Compute useful summary statistics from a data object. | prepaffy prepdata |
