NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data
Version 1.8.0

NanoStringQCPro provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data -- i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.

AuthorDorothee Nickles <nickles.dorothee@gene.com>, Thomas Sandmann <sandmann.thomas@gene.com>, Robert Ziman <ziman.robert@gene.com>, Richard Bourgon <bourgon.richard@gene.com>
Bioconductor views Microarray Normalization Preprocessing QualityControl ReportWriting mRNAMicroarray
Date of publicationNone
MaintainerRobert Ziman <ziman.robert@gene.com>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("NanoStringQCPro")

Popular man pages

countsInBlankSamples_verticalPlot: Plot counts in blank samples (vertical orientation)
cutoffByMMAD: cutoffByMMAD
example_rccSet: NanoStringQCPro example dataset
fovPlot: Fields of view (FOV) plot
makeQCReport: Make NanoString QC report
myCols: myCols
panelCor: panelCor
See all...

All man pages Function index File listing

Man pages

addCodesetAnnotation: Add NanoString codeset annotation to an RccSet
addQCFlags: Add sample QC flags to an rccSet
allSumPlot: allSumPlot
assessHousekeeping: assessHousekeeping
bdPlot: Binding density plot
buildCodesetAnnotation: Build NanoString codeset annotation
checkRccSet: Check an RccSet
colByCovar: colByCovar
colByFun: colByFun
contentNorm: Content normalization
copyRccSet: Deep-copy a NanoString RccSet
countsInBlankSamples_verticalPlot: Plot counts in blank samples (vertical orientation)
ctrlsOverviewPlot: ctrlsOverviewPlot
ctrlsZprimePlot: ctrlsZprimePlot
cutoffByMMAD: cutoffByMMAD
cutoffByVar: cutoffByVar
dCoVar: dCoVar
densityPlot: densityPlot
example_rccSet: NanoStringQCPro example dataset
flagSamplesCount: flagSamplesCount
flagSamplesCtrl: flagSamplesCtrl
flagSamplesTech: flagSamplesTech
fovPlot: Fields of view (FOV) plot
geneClustering: Gene clustering heatmap
getBackground: Get background estimates for a NanoString RccSet
getBlankLabel: Get the SampleType value that indicates blank samples
getSpikeInInput: getSpikeInInput
iqrPlot: iqrPlot
lodAssess: lodAssess
lodPlot: lodPlot
makeQCReport: Make NanoString QC report
myCols: myCols
NanoStringQCPro: NanoStringQCPro
negCtrlsByLane: negCtrlsByLane
negCtrlsByLane_verticalPlot: Plot of negative controls by lane (vertical orientation)
negCtrlsPairs: negCtrlsPairs
negCtrlsPlot: negCtrlsPlot
newRccSet: Create a new RccSet object
nSolverBackground: nSolver Analysis Software background estimation
nSolverCsv.to.pdata_fdata_adata: nSolverCsv.to.pdata_fdata_fdata
panelCor: panelCor
pcaPlot: pcaPlot
pdata_fdata_adata.to.rccSet: pdata_fdata_adata.to.rccSet
posCtrlNorm: Positive control normalization
posNormFactPlot: posNormFactPlot
posR2Plot: posR2Plot
posRatioPlot: posRatioPlot
posSlopePlot: posSlopePlot
posSumVsAllSumPlot: posSumVsAllSumPlot
preprocRccSet: Preprocess an RccSet
presAbsCall: Presence/absence call
previewPNG: Create a preview of a PNG
rccFiles.to.pdata_fdata_adata: rccFiles.to.pdata_fdata_adata
RccSet: RccSet constructor methods
RccSet-class: RccSet class, derived from ExpressionSet
readCdrDesignData: Read .CSV containing CDR 'Design Data' extract
readRcc: Read an .RCC file
readRccBatch: Read RCC files
readRccCollectorToolExport: Read RCC Collector Tool Export
readRlf: Read RLF file
sampleClustering: Clustering by sample correlation
scatterPair: scatterPair
subtractBackground: Subtract background estimates for a NanoString RccSet
zfacFun: zfacFun

Functions

.RccSet Man page
NAifNULL Source code
NanoStringQCPro Man page
NanoStringQCPro-package Man page
RccSet Man page
RccSet,ExpressionSet-method Man page
RccSet,environment-method Man page
RccSet,matrix-method Man page
RccSet,missing-method Man page
RccSet-class Man page
addCodesetAnnotation Man page
addCodesetAnnotation,RccSet-method Man page
addQCFlags Man page
addQCFlags,RccSet-method Man page
allSumPlot Man page
allSumPlot,RccSet-method Man page
assessHousekeeping Man page
assessHousekeeping,RccSet-method Man page
bdPlot Man page
bdPlot,RccSet-method Man page
buildCodesetAnnotation Man page Source code
centeredSampleClustering Source code
checkRccSet Man page
checkRccSet,RccSet-method Man page
check_cols Source code
colByCovar Man page Source code
colByFun Man page Source code
contentNorm Man page
contentNorm,RccSet-method Man page
copyRccSet Man page
copyRccSet,RccSet-method Man page
countsInBlankSamples_verticalPlot Man page Source code
ctrlsOverviewPlot Man page
ctrlsOverviewPlot,RccSet-method Man page
ctrlsZprimePlot Man page
ctrlsZprimePlot,RccSet-method Man page
cutoffByMMAD Man page Source code
cutoffByVar Man page Source code
dCoVar Man page Source code
densityPlot Man page Source code
example_rccSet Man page
flagSamplesCount Man page
flagSamplesCount,RccSet-method Man page
flagSamplesCtrl Man page
flagSamplesCtrl,RccSet-method Man page
flagSamplesTech Man page
flagSamplesTech,RccSet-method Man page
fovPlot Man page
fovPlot,RccSet-method Man page
geneClustering Man page Source code
getBackground Man page
getBackground,RccSet-method Man page
getBlankLabel Man page
getBlankLabel,RccSet-method Man page
getSpikeInInput Man page Source code
iqrPlot Man page
iqrPlot,RccSet-method Man page
lodAssess Man page
lodAssess,RccSet-method Man page
lodPlot Man page
lodPlot,RccSet-method Man page
makeQCReport Man page
makeQCReport,RccSet-method Man page
myCols Man page Source code
nSolverBackground Man page
nSolverBackground,RccSet-method Man page
nSolverCsv.to.pdata_fdata_adata Man page Source code
negCtrlsByLane Man page
negCtrlsByLane,RccSet-method Man page
negCtrlsByLane_verticalPlot Man page Source code
negCtrlsPairs Man page
negCtrlsPairs,RccSet-method Man page
negCtrlsPlot Man page
negCtrlsPlot,RccSet-method Man page
newRccSet Man page Source code
panelCor Man page Source code
pcaPlot Man page Source code
pdata_fdata_adata.to.rccSet Man page Source code
posCtrlNorm Man page
posCtrlNorm,RccSet-method Man page
posNormFactPlot Man page
posNormFactPlot,RccSet-method Man page
posR2Plot Man page
posR2Plot,RccSet-method Man page
posRatioPlot Man page
posRatioPlot,RccSet-method Man page
posSlopePlot Man page
posSlopePlot,RccSet-method Man page
posSumVsAllSumPlot Man page
posSumVsAllSumPlot,RccSet-method Man page
preprocRccSet Man page
preprocRccSet,RccSet-method Man page
presAbsCall Man page
presAbsCall,RccSet-method Man page
previewPNG Man page Source code
rccFiles.to.pdata_fdata_adata Man page Source code
readCdrDesignData Man page Source code
readRcc Man page Source code
readRccBatch Man page Source code
readRccCollectorToolExport Man page Source code
readRlf Man page Source code
sampleClustering Man page
sampleClustering,RccSet-method Man page
scatterPair Man page Source code
subtractBackground Man page
subtractBackground,RccSet-method Man page
zfacFun Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/0_RccSet-class.R
R/BackgroundSubtractionFunctions.R
R/NanoStringConvenience.R
R/NanoStringQCPro-package.r
R/NanoStringQCreport.R
R/NanoStringQualityMetrics.R
R/example_rccSet.R
R/previewPNG.R
R/utils.R
build
build/vignette.rds
data
data/example_rccSet.rdata
inst
inst/doc
inst/doc/vignetteNanoStringQCPro.R
inst/doc/vignetteNanoStringQCPro.Rnw
inst/doc/vignetteNanoStringQCPro.pdf
inst/examples
inst/examples/main.R
inst/extdata
inst/extdata/CDR
inst/extdata/CDR/CDR-DesignData.csv
inst/extdata/RCC
inst/extdata/RCC/20140604_C1-unstim_C1-unstim_01.RCC
inst/extdata/RCC/20140604_C1-unstim_C1-unstim_03.RCC
inst/extdata/RCC/20140604_C1-unstim_C1-unstim_04.RCC
inst/extdata/RCC/20140604_C1-unstim_C1-unstim_05.RCC
inst/extdata/RCC/20140604_C1-unstim_C1-unstim_08.RCC
inst/extdata/RCC/20140604_C1-unstim_C1-unstim_12.RCC
inst/extdata/RCC/20140604_C2-unstim_C2-unstim_02.RCC
inst/extdata/RCC/20140604_C2-unstim_C2-unstim_04.RCC
inst/extdata/RCC/20140604_C2-unstim_C2-unstim_06.RCC
inst/extdata/RCC/20140604_C2-unstim_C2-unstim_10.RCC
inst/extdata/RCC/20140604_C2-unstim_C2-unstim_10_2.RCC
inst/extdata/RCC/20140604_C2-unstim_C2-unstim_11.RCC
inst/extdata/RCC/20140604_C2-unstim_C2-unstim_12.RCC
inst/extdata/RCC/20140604_C3-stim_C3-stim_01.RCC
inst/extdata/RCC/20140604_C3-stim_C3-stim_02.RCC
inst/extdata/RCC/20140604_C3-stim_C3-stim_04.RCC
inst/extdata/RCC/20140604_C3-stim_C3-stim_07.RCC
inst/extdata/RCC/20140604_C3-stim_C3-stim_09.RCC
inst/extdata/RCC/20140604_C3-stim_C3-stim_11.RCC
inst/extdata/RCC/20140604_C4-stim_C4-stim_03.RCC
inst/extdata/RCC/20140604_C4-stim_C4-stim_04.RCC
inst/extdata/RCC/20140604_C4-stim_C4-stim_06.RCC
inst/extdata/RCC/20140604_C4-stim_C4-stim_07.RCC
inst/extdata/RCC/20140604_C4-stim_C4-stim_10.RCC
inst/extdata/RCC/20140604_C4-stim_C4-stim_12.RCC
inst/extdata/RLF
inst/extdata/RLF/NQCP_example.rlf
inst/extdata/extraPdata
inst/extdata/extraPdata/SampleType.txt
inst/extdata/nSolver
inst/extdata/nSolver/RCC_collector_tool_export.csv
inst/misc
inst/misc/qcReportHeader.html
inst/templates
inst/templates/QualityControlReportTemplate.Rmd
man
man/NanoStringQCPro.Rd
man/RccSet-class.Rd
man/RccSet.Rd
man/addCodesetAnnotation.Rd
man/addQCFlags.Rd
man/allSumPlot.Rd
man/assessHousekeeping.Rd
man/bdPlot.Rd
man/buildCodesetAnnotation.Rd
man/checkRccSet.Rd
man/colByCovar.Rd
man/colByFun.Rd
man/contentNorm.Rd
man/copyRccSet.Rd
man/countsInBlankSamples_verticalPlot.Rd
man/ctrlsOverviewPlot.Rd
man/ctrlsZprimePlot.Rd
man/cutoffByMMAD.Rd
man/cutoffByVar.Rd
man/dCoVar.Rd
man/densityPlot.Rd
man/example_rccSet.Rd
man/flagSamplesCount.Rd
man/flagSamplesCtrl.Rd
man/flagSamplesTech.Rd
man/fovPlot.Rd
man/geneClustering.Rd
man/getBackground.Rd
man/getBlankLabel.Rd
man/getSpikeInInput.Rd
man/iqrPlot.Rd
man/lodAssess.Rd
man/lodPlot.Rd
man/makeQCReport.Rd
man/myCols.Rd
man/nSolverBackground.Rd
man/nSolverCsv.to.pdata_fdata_adata.Rd
man/negCtrlsByLane.Rd
man/negCtrlsByLane_verticalPlot.Rd
man/negCtrlsPairs.Rd
man/negCtrlsPlot.Rd
man/newRccSet.Rd
man/panelCor.Rd
man/pcaPlot.Rd
man/pdata_fdata_adata.to.rccSet.Rd
man/posCtrlNorm.Rd
man/posNormFactPlot.Rd
man/posR2Plot.Rd
man/posRatioPlot.Rd
man/posSlopePlot.Rd
man/posSumVsAllSumPlot.Rd
man/preprocRccSet.Rd
man/presAbsCall.Rd
man/previewPNG.Rd
man/rccFiles.to.pdata_fdata_adata.Rd
man/readCdrDesignData.Rd
man/readRcc.Rd
man/readRccBatch.Rd
man/readRccCollectorToolExport.Rd
man/readRlf.Rd
man/sampleClustering.Rd
man/scatterPair.Rd
man/subtractBackground.Rd
man/zfacFun.Rd
vignettes
vignettes/NanoStringQCProOverview.pdf
vignettes/vignetteNanoStringQCPro.Rnw
NanoStringQCPro documentation built on May 20, 2017, 10:29 p.m.

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