Man pages for NanoStringQCPro
Quality metrics and data processing methods for NanoString mRNA gene expression data
| 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 |
