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
NanoStringQCPro         NanoStringQCPro
negCtrlsByLane_verticalPlot
                        Plot of negative controls by lane (vertical
                        orientation)
negCtrlsByLane,RccSet-method
                        negCtrlsByLane
negCtrlsPairs,RccSet-method
                        negCtrlsPairs
negCtrlsPlot,RccSet-method
                        negCtrlsPlot
newRccSet               Create a new RccSet object
nSolverBackground,RccSet-method
                        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,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
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,RccSet-method
                        Clustering by sample correlation
scatterPair             scatterPair
subtractBackground,RccSet-method
                        Subtract background estimates for a NanoString
                        RccSet
zfacFun                 zfacFun
