Package: arrayQuality 1.85.0

Agnes Paquet

arrayQuality: Assessing array quality on spotted arrays

Functions for performing print-run and array level quality assessment.

Authors:Agnes Paquet and Jean Yee Hwa Yang <[email protected]>

arrayQuality_1.85.0.tar.gz
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arrayQuality.pdf |arrayQuality.html✨
arrayQuality/json (API)

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

Peer review:

Datasets:
  • HsReferenceDB - Reference slides for Mouse oligos hybridizations
  • MmDEGenes - Known DE genes for Mouse quality hybridizations.
  • MmReferenceDB - Reference slides for Mouse oligos hybridizations

On BioConductor:arrayQuality-1.85.0(bioc 3.21)arrayQuality-1.84.0(bioc 3.20)

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

microarraytwochannelqualitycontrolvisualization

3.30 score 9 scripts 515 downloads 10 mentions 28 exports 7 dependencies

Last updated 2 months agofrom:b1c3550efe. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-winWARNINGDec 21 2024
R-4.5-linuxWARNINGDec 21 2024
R-4.4-winWARNINGDec 21 2024
R-4.4-macWARNINGDec 21 2024
R-4.3-winWARNINGDec 21 2024
R-4.3-macWARNINGDec 21 2024

Exports:agQualitycontrolCodeHeebocontrolCodeMeeboEMSplitgetSpikeIdsgetSpikeIndexglobalQualitygpQualityheeboQualityheeboQualityPlotsHeeboSpotTypesmaQualityPlotsmeeboQualitymeeboQualityPlotsMeeboSpotTypesPRv9mersPRvQCHybqcScorequalBoxplotqualityScorereadAgilentreadcontrolCodereadGPRreadSpikeTypesreadSpotscaleRefTableslideQualityspotQuality

Dependencies:gridBasehexbinlatticelimmamarrayRColorBrewerstatmod

Readme and manuals

Help Manual

Help pageTopics
Diagnostic plots and comparative boxplots for general hybridization, Agilent formatagcontrolCode agQuality
Quality measures for general hybridization.globalQuality
Diagnostic plots and comparative boxplots for general hybridizationgpQuality
Reference slides for Mouse oligos hybridizationsHsReferenceDB index.html MmReferenceDB
Diagnostics plots designed for HEEBO set controlsheeboQuality
Qualitative diagnostic plot for general hybridization, specific to HEEBO set.heeboQualityPlots
Internal arrayQuality functionsarrayControls arrayReplicates arrayScal BEbin.linear controlCodeHeebo controlCodeMeebo EMSplit getSpikeIds getSpikeIndex gpFlagWt HeeboSpotTypes MeeboSpotTypes outputNormData qpBEplot.linear qpBoxplotMeebo qpDotPlots qpDotPlotsEEBO qpDotPlotsMeebo qpDotPlotsMeebo2 qpHexbin qpImage qpMAPlots qpMisMatchPlot qpPTLoess qpS2N qpS2Neebo qpS2Nmeebo qpTiling quality2HTML readAllSpikes replicatesAvariance setCtlCol Spike.Cy5vsCy3 Spike.Individual.Sensitivity Spike.MM.Scatter Spike.MMplot Spike.Sensitivity
Qualitative diagnostic plot for general hybridizationmaQualityPlots
Diagnostics plots designed for MEEBO set controlsmeeboQuality
Qualitative diagnostic plot for general hybridization, specific to MEEBO set.meeboQualityPlots
Known DE genes for Mouse quality hybridizations.MmDEGenes
Example GPR files12Mm250.gpr 9Mm137.gpr
Print Run Quality version 9mersPRv9mers
Print run Quality version Quality Control HybridizationPRvQCHyb
Quality Control score for general hybridizationqcScore
Comparative boxplot for general hybridization Quality ControlqualBoxplot
Quality Control score for general hybridizationqualityScore
Extraction of measures from Agilent (.txt) files.readAgilent
Control status informationreadcontrolCode
Reading GenePix gpr filereadGPR
Read Spike Types FilereadSpikeTypes
Extraction of measures from Spot (.spot) files.readSpot
General hybridization quality scalingscaleRefTable
Quality Control statistics for general hybridizationslideQuality
Diagnostic plots and comparative boxplots for general hybridization, Spot formatspotQuality