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