Package: arrayMvout 1.71.0

V. Carey

arrayMvout: multivariate outlier detection for expression array QA

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate

Authors:Z. Gao, A. Asare, R. Wang, V. Carey

arrayMvout_1.71.0.tar.gz
arrayMvout_1.71.0.zip(r-4.7)arrayMvout_1.71.0.zip(r-4.6)arrayMvout_1.71.0.zip(r-4.5)
arrayMvout_1.71.0.tgz(r-4.6-any)arrayMvout_1.71.0.tgz(r-4.5-any)
arrayMvout_1.71.0.tar.gz(r-4.7-any)arrayMvout_1.71.0.tar.gz(r-4.6-any)
arrayMvout_1.71.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
arrayMvout/json (API)

# Install 'arrayMvout' in R:
install.packages('arrayMvout', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • afxsubDEG - Multivariate outlier detection based on PCA of QA statistics
  • fig3map - Multivariate outlier detection based on PCA of QA statistics
  • ilmQA - Multivariate outlier detection based on PCA of QA statistics
  • itnQA - Multivariate outlier detection based on PCA of QA statistics
  • maqcQA - Multivariate outlier detection based on PCA of QA statistics
  • s12cDEG - Multivariate outlier detection based on PCA of QA statistics
  • spikQA - Multivariate outlier detection based on PCA of QA statistics

On BioConductor:arrayMvout-1.71.0(bioc 3.24)arrayMvout-1.70.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructuremicroarrayqualitycontrol

3.82 score 11 scripts 536 downloads 3 mentions 3 exports 163 dependencies

Last updated from:721aff7494. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR388
linux-devel-x86_64NOTE683
source / vignettesOK511
linux-release-x86_64NOTE649
macos-release-arm64NOTE356
macos-oldrel-arm64NOTE330
windows-develNOTE487
windows-releaseNOTE467
windows-oldrelNOTE499
wasm-releaseOK349

Exports:ArrayOutliersplotshow

Dependencies:abindaffyaffyContamaffydataaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicliprclustercodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrfarverfastmapFDb.InfiniumMethylation.hg19filelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitlumimagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmdqcmemoisemethylumimgcvmimeminfimulttestnleqslvnlmenor1mixopensslorg.Hs.eg.dbparodypillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryaml

arrayMvout -- multivariate outlier algorithm for expression arrays

Rendered fromarrayMvout.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2020-12-08
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Multivariate outlier detection based on PCA of QA statisticsafxsubDEG afxsubQC ArrayOutliers fig3map ILM1 ilmQA itnQA maqcQA s12c s12cDEG s12cQC spikQA
ArrayOutliers - wrapper for platform-specific multivariate outlier detection for expression arraysArrayOutliers,AffyBatch,numeric,ANY-method ArrayOutliers,ANY,missing,missing-method ArrayOutliers,data.frame,numeric,ANY-method ArrayOutliers,LumiBatch,numeric,ANY-method ArrayOutliers-methods
Class "arrOutStruct" container for ArrayOutliers outputarrOutStruct-class plot,arrOutStruct,ANY-method show,arrOutStruct-method