![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg){kind=small}
![[Top]](../../../doc/html/up.jpg){kind=small}
A B C D E F G H I L M N P Q R S T U V W X
| xps-package | xps Package Overview |
| addData | Import additional CEL files into a DataTreeSet |
| addData-method | Class DataTreeSet |
| addData-methods | Import additional CEL files into a DataTreeSet |
| AffyRNAdeg | Functions to assess RNA Degradation. |
| AnalysisTreeSet | Class AnalysisTreeSet |
| AnalysisTreeSet-class | Class AnalysisTreeSet |
| arrayInfo | Class ProjectInfo |
| arrayInfo-method | Class ProjectInfo |
| arrayInfo<- | Class ProjectInfo |
| arrayInfo<--method | Class ProjectInfo |
| attachBgrd | Attach/Remove Background Intensities |
| attachBgrd-method | Class DataTreeSet |
| attachBgrd-methods | Attach/Remove Background Intensities |
| attachCall | Attach/Remove Detecion Call Measures |
| attachCall-method | Class CallTreeSet |
| attachCall-methods | Attach/Remove Detecion Call Measures |
| attachData | Attach/Remove Data |
| attachData-method | Class ProcesSet |
| attachData-methods | Attach/Remove Data |
| attachDataXY | Attach/Remove (X,Y)-Coordinates |
| attachDataXY-method | Class DataTreeSet |
| attachDataXY-methods | Attach/Remove (X,Y)-Coordinates |
| attachExpr | Attach/Remove Expression Measures |
| attachExpr-method | Class ExprTreeSet |
| attachExpr-methods | Attach/Remove Expression Measures |
| attachInten | Attach/Remove Intensities |
| attachInten-method | Class DataTreeSet |
| attachInten-methods | Attach/Remove Intensities |
| attachMask | Attach/Remove Scheme Mask |
| attachMask-method | Class DataTreeSet |
| attachMask-method | Class SchemeTreeSet |
| attachMask-methods | Attach/Remove Scheme Mask |
| attachProbe | Attach/Remove Probe Sequence and/or GC Content |
| attachProbe-method | Class SchemeTreeSet |
| attachProbe-methods | Attach/Remove Probe Sequence and/or GC Content |
| attachProbeContentGC | Attach/Remove Probe Sequence and/or GC Content |
| attachProbeContentGC-method | Class DataTreeSet |
| attachProbeContentGC-method | Class SchemeTreeSet |
| attachProbeContentGC-methods | Attach/Remove Probe Sequence and/or GC Content |
| attachProbeSequence | Attach/Remove Probe Sequence and/or GC Content |
| attachProbeSequence-method | Class SchemeTreeSet |
| attachPVal | Attach/Remove Detecion Call Measures |
| attachPVal-method | Class CallTreeSet |
| attachPVal-methods | Attach/Remove Detecion Call Measures |
| attachUnitNames | Attach/Remove Unit Names |
| attachUnitNames-method | Class DataTreeSet |
| attachUnitNames-method | Class SchemeTreeSet |
| attachUnitNames-methods | Attach/Remove Unit Names |
| authorInfo | Class ProjectInfo |
| authorInfo-method | Class ProjectInfo |
| authorInfo<- | Class ProjectInfo |
| authorInfo<--method | Class ProjectInfo |
| background | Class DataTreeSet |
| background-method | Class DataTreeSet |
| background<- | Class DataTreeSet |
| background<--method | Class DataTreeSet |
| bgcorrect | Background Correction |
| bgcorrect.gc | Background Correction |
| bgcorrect.mas4 | Background Correction |
| bgcorrect.mas5 | Background Correction |
| bgcorrect.rma | Background Correction |
| bgtreeNames | Class DataTreeSet |
| bgtreeNames-method | Class DataTreeSet |
| biopsyInfo | Class ProjectInfo |
| biopsyInfo-method | Class ProjectInfo |
| biopsyInfo<- | Class ProjectInfo |
| biopsyInfo<--method | Class ProjectInfo |
| borderplot | Plots of Border Elements |
| borderplot-method | Class QualTreeSet |
| borderplot-methods | Plots of Border Elements |
| borders | Class QualTreeSet |
| borders-method | Class QualTreeSet |
| boxplot | Box Plots |
| boxplot-method | Class ProcesSet |
| boxplot-methods | Box Plots |
| callFilter | Detection Call Filter |
| callFilter-method | Class PreFilter |
| callFilter-method | Class UniFilter |
| callFilter-methods | Detection Call Filter |
| callFilter<- | Detection Call Filter |
| callFilter<--method | Class PreFilter |
| callFilter<--method | Class UniFilter |
| callplot | Barplot of Percent Present and Absent Calls. |
| callplot-method | Class CallTreeSet |
| callplot-methods | Barplot of Percent Present and Absent Calls. |
| CallTreeSet | Class CallTreeSet |
| callTreeset | Class FilterTreeSet |
| CallTreeSet-class | Class CallTreeSet |
| callTreeset-method | Class FilterTreeSet |
| cellineInfo | Class ProjectInfo |
| cellineInfo-method | Class ProjectInfo |
| cellineInfo<- | Class ProjectInfo |
| cellineInfo<--method | Class ProjectInfo |
| chipMask | Class SchemeTreeSet |
| chipMask-method | Class SchemeTreeSet |
| chipMask<- | Class SchemeTreeSet |
| chipMask<--method | Class SchemeTreeSet |
| chipName | Class SchemeTreeSet |
| chipName-method | Class ProcesSet |
| chipName-method | Class SchemeTreeSet |
| chipProbe | Class SchemeTreeSet |
| chipProbe-method | Class SchemeTreeSet |
| chipProbe<- | Class SchemeTreeSet |
| chipProbe<--method | Class SchemeTreeSet |
| chipType | Class SchemeTreeSet |
| chipType-method | Class ProcesSet |
| chipType-method | Class SchemeTreeSet |
| chipType<- | Class SchemeTreeSet |
| chipType<--method | Class SchemeTreeSet |
| coiplot | Center-Of-Intensity QC Plots |
| coiplot-method | Class QualTreeSet |
| coiplot-methods | Center-Of-Intensity QC Plots |
| corplot | Array-Array Expression Level Correlation Plot |
| corplot-method | Class ExprTreeSet |
| corplot-methods | Array-Array Expression Level Correlation Plot |
| cvFilter | Coefficient of Variation Filter |
| cvFilter-method | Class PreFilter |
| cvFilter-methods | Coefficient of Variation Filter |
| cvFilter<- | Coefficient of Variation Filter |
| cvFilter<--method | Class PreFilter |
| dabg.call | Detection Above Background Call |
| datasetInfo | Class ProjectInfo |
| datasetInfo-method | Class ProjectInfo |
| datasetInfo<- | Class ProjectInfo |
| datasetInfo<--method | Class ProjectInfo |
| DataTreeSet | Class DataTreeSet |
| DataTreeSet-class | Class DataTreeSet |
| debug.xps | xps Options |
| dfw | Distribution Free Weighted Expression Measure |
| diffFilter | Difference Filter |
| diffFilter-method | Class PreFilter |
| diffFilter-methods | Difference Filter |
| diffFilter<- | Difference Filter |
| diffFilter<--method | Class PreFilter |
| existsROOTFile | Test for Existing ROOT File |
| exonLevel | Conversion of Parameter exonlevel to Integer |
| export | Export data as text files |
| export-method | Class ProcesSet |
| export-method | Class SchemeTreeSet |
| export-method | Class TreeSet |
| export-methods | Export data as text files |
| export.call | Export data as text files |
| export.data | Export data as text files |
| export.expr | Export data as text files |
| export.filter | Export filter data as text files |
| export.root | Export data from ROOT file |
| export.scheme | Export data as text files |
| express | Compute expression levels from raw data |
| exprs | Get/Set Expression Values |
| exprs-method | Class ExprTreeSet |
| exprs-methods | Get/Set Expression Values |
| exprs<- | Get/Set Expression Values |
| exprs<--method | Class ExprTreeSet |
| ExprTreeSet | Class ExprTreeSet |
| exprTreeset | Class FilterTreeSet |
| ExprTreeSet-class | Class ExprTreeSet |
| exprTreeset-method | Class FilterTreeSet |
| exprType | Class ExprTreeSet |
| exprType-method | Class ExprTreeSet |
| exprType<- | Class ExprTreeSet |
| exprType<--method | Class ExprTreeSet |
| extenPart | Get Extension of Tree Names |
| farms | Factor Analysis for Robust Microarray Summarization Expression Measure |
| fcFilter | Fold-Change Filter |
| fcFilter-method | Class UniFilter |
| fcFilter-methods | Fold-Change Filter |
| fcFilter<- | Fold-Change Filter |
| fcFilter<--method | Class UniFilter |
| fileDir | Class TreeSet |
| fileDir-method | Class TreeSet |
| fileDir<- | Class TreeSet |
| fileDir<--method | Class TreeSet |
| Filter-class | Base Class Filter |
| FilterTreeSet | Class FilterTreeSet |
| filterTreeset | Class AnalysisTreeSet |
| FilterTreeSet-class | Class FilterTreeSet |
| filterTreeset-method | Class AnalysisTreeSet |
| firma | Finding Isoforms using Robust Multichip Analysis |
| firma.expr | Get Expression Levels from FIRMA |
| firma.score | Get Splice Score from FIRMA |
| fitQC | Functions for fitting probe-level models |
| fitRLM | Functions for fitting RMA as probe-level model |
| gapFilter | Gap Filter |
| gapFilter-method | Class PreFilter |
| gapFilter-methods | Gap Filter |
| gapFilter<- | Gap Filter |
| gapFilter<--method | Class PreFilter |
| getChipName | Get Chip Name |
| getChipType | Get Chip Type |
| getDatatype | Get Data Type |
| getNameType | Get Chip Name and Type |
| getNumberTrees | Get Number of Trees |
| getProbeInfo | Get Probe Information |
| getTreeData | Export Tree Data |
| getTreeData-method | Class AnalysisTreeSet |
| getTreeData-method | Class FilterTreeSet |
| getTreeData-method | Class ProcesSet |
| getTreeData-methods | Export Tree Data |
| getTreeNames | Get Tree Names |
| highFilter | Upper Threshold Filter |
| highFilter-method | Class PreFilter |
| highFilter-methods | Upper Threshold Filter |
| highFilter<- | Upper Threshold Filter |
| highFilter<--method | Class PreFilter |
| hist | Plot Density Estimate |
| hist-method | Class DataTreeSet |
| hist-method | Class ProcesSet |
| hist-methods | Plot Density Estimate |
| hybridizInfo | Class ProjectInfo |
| hybridizInfo-method | Class ProjectInfo |
| hybridizInfo<- | Class ProjectInfo |
| hybridizInfo<--method | Class ProjectInfo |
| image | Display an Image |
| image-method | Class ProcesSet |
| image-method | Class QualTreeSet |
| image-methods | Display an Image |
| import.data | Import CEL files into a DataTreeSet |
| import.exon.scheme | Import CLF, PGF and annotation files into a SchemeTreeSet |
| import.expr.scheme | Import CDF, probe and annotation files into a SchemeTreeSet |
| import.genome.scheme | Import CLF, PGF and annotation files into a SchemeTreeSet |
| indexUnits | Unit Locations |
| indexUnits-method | Class DataTreeSet |
| indexUnits-methods | Unit Locations |
| ini.call | Informative/Non-Informative Call |
| initialize | Initialize Classes |
| initialize-method | Initialize Classes |
| initialize-methods | Initialize Classes |
| intensity | Get/Set Data Values |
| intensity-method | Class DataTreeSet |
| intensity-methods | Get/Set Data Values |
| intensity2GCplot | Boxlot of Probe Intensities Stratified by GC Content. |
| intensity2GCplot-method | Class DataTreeSet |
| intensity2GCplot-methods | Boxlot of Probe Intensities Stratified by GC Content. |
| intensity<- | Get/Set Data Values |
| intensity<--method | Class DataTreeSet |
| isROOTFile | Test for ROOT File |
| lowFilter | Lower Threshold Filter |
| lowFilter-method | Class PreFilter |
| lowFilter-methods | Lower Threshold Filter |
| lowFilter<- | Lower Threshold Filter |
| lowFilter<--method | Class PreFilter |
| madFilter | Median Absolute Deviation Filter |
| madFilter-method | Class PreFilter |
| madFilter-methods | Median Absolute Deviation Filter |
| madFilter<- | Median Absolute Deviation Filter |
| madFilter<--method | Class PreFilter |
| madplot | Array-Array Expression Level Distance Plot |
| madplot-method | Class ExprTreeSet |
| madplot-methods | Array-Array Expression Level Distance Plot |
| mas4 | MAS 4.0 Expression Measure |
| mas5 | MAS 5.0 Expression Measure |
| mas5.call | MAS 5.0 Absolute Detection Call |
| mboxplot | Box Plots of Relative M Values |
| mboxplot-method | Class ProcesSet |
| mboxplot-methods | Box Plots of Relative M Values |
| metaProbesets | Create MetaProbeset File for APT |
| mm | Methods for accessing perfect matches and mismatches |
| mm-method | Class DataTreeSet |
| mm-methods | Methods for accessing perfect matches and mismatches |
| mmindex | Unit Locations |
| mmindex-method | Class DataTreeSet |
| mmindex-methods | Unit Locations |
| mvaplot | M vs A Plot |
| mvaplot-method | Class ExprTreeSet |
| mvaplot-methods | M vs A Plot |
| namePart | Get Tree Names w/o Extension |
| ncols | Class SchemeTreeSet |
| ncols-method | Class DataTreeSet |
| ncols-method | Class SchemeTreeSet |
| normalize | Normalization on Affymetrix Probe Level Data or on Expression Levels |
| normalize.constant | Normalization on Affymetrix Probe Level Data or on Expression Levels |
| normalize.lowess | Normalization on Affymetrix Probe Level Data or on Expression Levels |
| normalize.quantiles | Normalization on Affymetrix Probe Level Data or on Expression Levels |
| normalize.supsmu | Normalization on Affymetrix Probe Level Data or on Expression Levels |
| normType | Class ExprTreeSet |
| normType-method | Class ExprTreeSet |
| normType<- | Class ExprTreeSet |
| normType<--method | Class ExprTreeSet |
| nrows | Class SchemeTreeSet |
| nrows-method | Class DataTreeSet |
| nrows-method | Class SchemeTreeSet |
| numberFilters | Base Class Filter |
| numberFilters-method | Base Class Filter |
| NUSE | Normalized Unscaled Standard Errors (NUSE) |
| NUSE-method | Class QualTreeSet |
| NUSE-methods | Normalized Unscaled Standard Errors (NUSE) |
| nuseplot | Box Plots of Normalized Unscaled Standard Errors (NUSE) |
| nuseplot-method | Class ExprTreeSet |
| nuseplot-method | Class QualTreeSet |
| nuseplot-methods | Box Plots of Normalized Unscaled Standard Errors (NUSE) |
| pcaplot | PCA Plot |
| pcaplot-method | Class ExprTreeSet |
| pcaplot-methods | PCA Plot |
| plotAffyRNAdeg | Functions to assess RNA Degradation. |
| plotBorder | Plots of Border Elements for Device |
| plotBoxplot | Box Plots for Device |
| plotCall | Barplot of Percent Present and Absent Calls for Device |
| plotCOI | Center-Of-Intensity QC Plots for Device |
| plotCorr | Array-Array Expression Level Correlation Plot for Device |
| plotDensity | Plot Density Estimate for Device |
| plotImage | Plot Image(s) for Device |
| plotIntensity2GC | Boxlot of Probe Intensities Stratified by GC Content for Device. |
| plotMA | MvA Scatter Plot for Device |
| plotMAD | Array-Array Expression Level Distance Plot for Device |
| plotNUSE | Box Plots of Normalized Unscaled Standard Errors (NUSE) for Device |
| plotPCA | PCA Plot for Device |
| plotPM | Barplot of PM and MM Intensities for Device |
| plotProbeset | Plot of Probe Intensities for a Probeset for Device. |
| plotRLE | Box Plots of Relative Log Expression (RLE) for Device |
| plotVolcano | Volcano Plot |
| pm | Methods for accessing perfect matches and mismatches |
| pm-method | Class DataTreeSet |
| pm-methods | Methods for accessing perfect matches and mismatches |
| pmindex | Unit Locations |
| pmindex-method | Class DataTreeSet |
| pmindex-methods | Unit Locations |
| pmplot | Barplot of PM and MM Intensities. |
| pmplot-method | Class DataTreeSet |
| pmplot-methods | Barplot of PM and MM Intensities. |
| PreFilter | Constructor for Class PreFilter |
| prefilter | Function for Applying a PreFilter to an ExprTreeSet |
| PreFilter-class | Class PreFilter |
| presCall | Get/Set Present Call Values |
| presCall-method | Class CallTreeSet |
| presCall-methods | Get/Set Present Call Values |
| presCall<- | Get/Set Present Call Values |
| presCall<--method | Class CallTreeSet |
| primcellInfo | Class ProjectInfo |
| primcellInfo-method | Class ProjectInfo |
| primcellInfo<- | Class ProjectInfo |
| primcellInfo<--method | Class ProjectInfo |
| probeContentGC | Get G/C Content for Probes |
| probeContentGC-method | Class SchemeTreeSet |
| probeContentGC-methods | Get G/C Content for Probes |
| probeInfo | Class SchemeTreeSet |
| probeInfo-method | Class SchemeTreeSet |
| probeSequence | Get Probe Sequence |
| probeSequence-method | Class SchemeTreeSet |
| probeSequence-methods | Get Probe Sequence |
| probesetID2unitID | Conversion between Probeset IDs and UnitIDs |
| probesetID2unitID-method | Class DataTreeSet |
| probesetID2unitID-method | Class SchemeTreeSet |
| probesetID2unitID-methods | Conversion between Probeset IDs and UnitIDs |
| probesetplot | Plot of Probe Intensities for a Probeset. |
| probesetplot-method | Class DataTreeSet |
| probesetplot-methods | Plot of Probe Intensities for a Probeset. |
| ProcesSet | Class ProcesSet |
| ProcesSet-class | Class ProcesSet |
| ProjectInfo | Constructor for Class ProjectInfo |
| projectInfo | Class ProjectInfo |
| ProjectInfo-class | Class ProjectInfo |
| projectInfo-method | Class DataTreeSet |
| projectInfo-method | Class ProjectInfo |
| projectInfo<- | Class ProjectInfo |
| projectInfo<--method | Class DataTreeSet |
| projectInfo<--method | Class ProjectInfo |
| pvalData | Get/Set Present Call Values |
| pvalData-method | Class CallTreeSet |
| pvalData-methods | Get/Set Present Call Values |
| pvalData<- | Get/Set Present Call Values |
| pvalData<--method | Class CallTreeSet |
| qualify | Probe Set Quality Control Functions |
| qualify.rlm | Probe Set Quality Control Functions |
| qualOption | Class QualTreeSet |
| qualOption-method | Class QualTreeSet |
| qualOption<- | Class QualTreeSet |
| qualOption<--method | Class QualTreeSet |
| QualTreeSet | Class QualTreeSet |
| QualTreeSet-class | Class QualTreeSet |
| qualType | Class QualTreeSet |
| qualType-method | Class QualTreeSet |
| qualType<- | Class QualTreeSet |
| qualType<--method | Class QualTreeSet |
| quantileFilter | Quantile Filter |
| quantileFilter-method | Class PreFilter |
| quantileFilter-methods | Quantile Filter |
| quantileFilter<- | Quantile Filter |
| quantileFilter<--method | Class PreFilter |
| ratioFilter | Ratio Filter |
| ratioFilter-method | Class PreFilter |
| ratioFilter-methods | Ratio Filter |
| ratioFilter<- | Ratio Filter |
| ratioFilter<--method | Class PreFilter |
| rawCELName | Method for getting names of the raw CEL-files |
| rawCELName-method | Class DataTreeSet |
| rawCELName-methods | Method for getting names of the raw CEL-files |
| removeBgrd | Attach/Remove Background Intensities |
| removeBgrd-method | Class DataTreeSet |
| removeBgrd-methods | Attach/Remove Background Intensities |
| removeCall | Attach/Remove Detecion Call Measures |
| removeCall-method | Class CallTreeSet |
| removeCall-methods | Attach/Remove Detecion Call Measures |
| removeData | Attach/Remove Data |
| removeData-method | Class ProcesSet |
| removeData-methods | Attach/Remove Data |
| removeDataXY | Attach/Remove (X,Y)-Coordinates |
| removeDataXY-method | Class DataTreeSet |
| removeDataXY-methods | Attach/Remove (X,Y)-Coordinates |
| removeExpr | Attach/Remove Expression Measures |
| removeExpr-method | Class ExprTreeSet |
| removeExpr-methods | Attach/Remove Expression Measures |
| removeInten | Attach/Remove Intensities |
| removeInten-method | Class DataTreeSet |
| removeInten-methods | Attach/Remove Intensities |
| removeMask | Attach/Remove Scheme Mask |
| removeMask-method | Class DataTreeSet |
| removeMask-method | Class SchemeTreeSet |
| removeMask-methods | Attach/Remove Scheme Mask |
| removeProbe | Attach/Remove Probe Sequence and/or GC Content |
| removeProbe-method | Class SchemeTreeSet |
| removeProbeContentGC | Attach/Remove Probe Sequence and/or GC Content |
| removeProbeContentGC-method | Class DataTreeSet |
| removeProbeContentGC-method | Class SchemeTreeSet |
| removeProbeContentGC-methods | Attach/Remove Probe Sequence and/or GC Content |
| removeProbeSequence | Attach/Remove Probe Sequence and/or GC Content |
| removeProbeSequence-method | Class SchemeTreeSet |
| removeProbeSequence-methods | Attach/Remove Probe Sequence and/or GC Content |
| removePVal | Attach/Remove Detecion Call Measures |
| removePVal-method | Class CallTreeSet |
| removePVal-methods | Attach/Remove Detecion Call Measures |
| removeUnitNames | Attach/Remove Unit Names |
| removeUnitNames-method | Class DataTreeSet |
| removeUnitNames-method | Class SchemeTreeSet |
| removeUnitNames-methods | Attach/Remove Unit Names |
| residuals | Class QualTreeSet |
| residuals-method | Class QualTreeSet |
| RLE | Relative Log Expression (RLE) |
| RLE-method | Class QualTreeSet |
| RLE-methods | Relative Log Expression (RLE) |
| rleplot | Box Plots of Relative Log Expression (RLE) |
| rleplot-method | Class ExprTreeSet |
| rleplot-method | Class QualTreeSet |
| rleplot-methods | Box Plots of Relative Log Expression (RLE) |
| rma | Robust Multi-Array Average Expression Measure |
| rmaPLM | Functions for fitting RMA as probe-level model |
| ROOT | ROOT An Object-Oriented Data Analysis Framework |
| root.browser | Open the ROOT object browser |
| root.browser-method | Class TreeSet |
| root.call | Create class CallTreeSet accessing ROOT detection call file |
| root.data | Create class DataTreeSet accessing ROOT data file |
| root.density | ROOT Density Plot |
| root.expr | Create class ExprTreeSet accessing ROOT expression file |
| root.graph1D | ROOT 1D-Graph |
| root.graph2D | ROOT 2D-Graph |
| root.hist1D | ROOT 1D-Histogram |
| root.hist2D | ROOT 2D-Histogram |
| root.hist3D | ROOT 3D-Histogram |
| root.image | ROOT Image |
| root.merge.data | Create class DataTreeSet by merging ROOT data files |
| root.mvaplot | ROOT M vs A Plot |
| root.profile | ROOT Profile Plot |
| root.scheme | Create class SchemeTreeSet accessing ROOT scheme file |
| rootFile | Class TreeSet |
| rootFile-method | Class TreeSet |
| rootFile<- | Class TreeSet |
| rootFile<--method | Class TreeSet |
| sampleInfo | Class ProjectInfo |
| sampleInfo-method | Class ProjectInfo |
| sampleInfo<- | Class ProjectInfo |
| sampleInfo<--method | Class ProjectInfo |
| schemeFile | Class ProcesSet |
| schemeFile-method | Class ProcesSet |
| schemeFile<- | Class ProcesSet |
| schemeFile<--method | Class ProcesSet |
| schemeSet | Class ProcesSet |
| schemeSet-method | Class ProcesSet |
| schemeSet<- | Class ProcesSet |
| schemeSet<--method | Class ProcesSet |
| SchemeTreeSet | Class SchemeTreeSet |
| SchemeTreeSet-class | Class SchemeTreeSet |
| se.exprs | Class ExprTreeSet |
| se.exprs-method | Class ExprTreeSet |
| setName | Class TreeSet |
| setName-method | Class TreeSet |
| setName<- | Class TreeSet |
| setName<--method | Class TreeSet |
| setType | Class TreeSet |
| setType-method | Class TreeSet |
| setType<- | Class TreeSet |
| setType<--method | Class TreeSet |
| show-method | Class ProjectInfo |
| sourceInfo | Class ProjectInfo |
| sourceInfo-method | Class ProjectInfo |
| sourceInfo<- | Class ProjectInfo |
| sourceInfo<--method | Class ProjectInfo |
| summarize | Probe Set Summarizing Functions |
| summarize.mas4 | Probe Set Summarizing Functions |
| summarize.mas5 | Probe Set Summarizing Functions |
| summarize.rma | Probe Set Summarizing Functions |
| summaryAffyRNAdeg | Functions to assess RNA Degradation. |
| symbol2unitID | Conversion between Gene Symbols and UnitIDs |
| symbol2unitID-method | Class DataTreeSet |
| symbol2unitID-method | Class SchemeTreeSet |
| symbol2unitID-methods | Conversion between Gene Symbols and UnitIDs |
| tissueInfo | Class ProjectInfo |
| tissueInfo-method | Class ProjectInfo |
| tissueInfo<- | Class ProjectInfo |
| tissueInfo<--method | Class ProjectInfo |
| transcriptID2unitID | Conversion between Probeset IDs and UnitIDs |
| transcriptID2unitID-method | Class DataTreeSet |
| transcriptID2unitID-method | Class SchemeTreeSet |
| transcriptID2unitID-methods | Conversion between Probeset IDs and UnitIDs |
| treatmentInfo | Class ProjectInfo |
| treatmentInfo-method | Class ProjectInfo |
| treatmentInfo<- | Class ProjectInfo |
| treatmentInfo<--method | Class ProjectInfo |
| treeData | Class ProcesSet |
| treeData-method | Class ProcesSet |
| treeInfo | Get UserInfo from ROOT Trees |
| treeInfo-method | Class TreeSet |
| treeInfo-methods | Get UserInfo from ROOT Trees |
| treeNames | Class TreeSet |
| treeNames-method | Class TreeSet |
| TreeSet | Class TreeSet |
| TreeSet-class | Class TreeSet |
| trma | transposed Robust Multi-Array Average Expression Measure |
| type2Exten | Convert Method Type to Tree Extension |
| UniFilter | Constructor for Class UniFilter |
| unifilter | Function for Applying an UniFilter to an ExprTreeSet |
| UniFilter-class | Class UniFilter |
| uniTest | A Two-Group Unitest |
| uniTest-method | Class UniFilter |
| uniTest-methods | A Two-Group Unitest |
| uniTest<- | A Two-Group Unitest |
| uniTest<--method | Class UniFilter |
| unitestFilter | Unitest Filter |
| unitestFilter-method | Class UniFilter |
| unitestFilter-methods | Unitest Filter |
| unitestFilter<- | Unitest Filter |
| unitestFilter<--method | Class UniFilter |
| unitID2probesetID | Conversion between Probeset IDs and UnitIDs |
| unitID2probesetID-method | Class DataTreeSet |
| unitID2probesetID-method | Class SchemeTreeSet |
| unitID2probesetID-methods | Conversion between Probeset IDs and UnitIDs |
| unitID2symbol | Conversion between Gene Symbols and UnitIDs |
| unitID2symbol-method | Class DataTreeSet |
| unitID2symbol-method | Class SchemeTreeSet |
| unitID2symbol-methods | Conversion between Gene Symbols and UnitIDs |
| unitID2transcriptID | Conversion between Probeset IDs and UnitIDs |
| unitID2transcriptID-method | Class DataTreeSet |
| unitID2transcriptID-method | Class SchemeTreeSet |
| unitID2transcriptID-methods | Conversion between Probeset IDs and UnitIDs |
| unitNames | Class SchemeTreeSet |
| unitNames-method | Class SchemeTreeSet |
| unitNames<- | Class SchemeTreeSet |
| unitNames<--method | Class SchemeTreeSet |
| validBgrd | Class DataTreeSet |
| validBgrd-method | Class DataTreeSet |
| validCall | Get Valid Detection Call Values |
| validCall-method | Class CallTreeSet |
| validData | Extract Subset of Data |
| validData-method | Class AnalysisTreeSet |
| validData-method | Class DataTreeSet |
| validData-method | Class FilterTreeSet |
| validData-method | Class ProcesSet |
| validExpr | Get Valid Expression Levels |
| validExpr-method | Class ExprTreeSet |
| validFilter | Class AnalysisTreeSet |
| validFilter-method | Class AnalysisTreeSet |
| validPVal | Get Valid Detection Call Values |
| validPVal-method | Class CallTreeSet |
| validSE | Get Valid Standard Errors |
| validSE-method | Class ExprTreeSet |
| validTreetype | Validate Tree Type |
| varFilter | Variance Filter |
| varFilter-method | Class PreFilter |
| varFilter-methods | Variance Filter |
| varFilter<- | Variance Filter |
| varFilter<--method | Class PreFilter |
| volcanoplot | Volcano Plot |
| volcanoplot-method | Class AnalysisTreeSet |
| volcanoplot-methods | Volcano Plot |
| weights | Class QualTreeSet |
| weights-method | Class QualTreeSet |
| xps | xps Package Overview |
| xpsBgCorrect | Background Correction |
| xpsBgCorrect-method | Class DataTreeSet |
| xpsBgCorrect-methods | Background Correction |
| xpsDABGCall | Detection Above Background Call |
| xpsDABGCall-method | Class DataTreeSet |
| xpsDABGCall-methods | Detection Above Background Call |
| xpsFIRMA | Finding Isoforms using Robust Multichip Analysis |
| xpsFIRMA-method | Class DataTreeSet |
| xpsFIRMA-methods | Finding Isoforms using Robust Multichip Analysis |
| xpsINICall | Informative/Non-Informative Call |
| xpsINICall-method | Class DataTreeSet |
| xpsINICall-methods | Informative/Non-Informative Call |
| xpsMAS4 | MAS 4.0 Expression Measure |
| xpsMAS4-method | Class DataTreeSet |
| xpsMAS4-methods | MAS 4.0 Expression Measure |
| xpsMAS5 | MAS 5.0 Expression Measure |
| xpsMAS5-method | Class DataTreeSet |
| xpsMAS5-methods | MAS 5.0 Expression Measure |
| xpsMAS5Call | MAS 5.0 Absolute Detection Call |
| xpsMAS5Call-method | Class DataTreeSet |
| xpsMAS5Call-methods | MAS 5.0 Absolute Detection Call |
| xpsNormalize | Normalization on Affymetrix Probe Level Data or on Expression Levels |
| xpsNormalize-method | Class DataTreeSet |
| xpsNormalize-method | Class ExprTreeSet |
| xpsNormalize-methods | Normalization on Affymetrix Probe Level Data or on Expression Levels |
| xpsOptions | xps Options |
| xpsPreFilter | Function for Applying a PreFilter to an ExprTreeSet |
| xpsPreFilter-method | Class ExprTreeSet |
| xpsPreFilter-methods | Function for Applying a PreFilter to an ExprTreeSet |
| xpsPreprocess | Compute expression levels from raw data |
| xpsPreprocess-method | Class DataTreeSet |
| xpsPreprocess-methods | Compute expression levels from raw data |
| xpsQAReport | Create Quality Assessment Report. |
| xpsQualify | Probe Set Quality Control Functions |
| xpsQualify-method | Class DataTreeSet |
| xpsQualify-methods | Probe Set Quality Control Functions |
| xpsQualityControl | Functions for fitting probe-level models |
| xpsQualityControl-method | Class DataTreeSet |
| xpsQualityControl-methods | Functions for fitting probe-level models |
| xpsRMA | Robust Multi-Array Average Expression Measure |
| xpsRMA-method | Class DataTreeSet |
| xpsRMA-methods | Robust Multi-Array Average Expression Measure |
| xpsRNAdeg | Functions to assess RNA Degradation. |
| xpsRNAdeg-method | Class QualTreeSet |
| xpsRNAdeg-methods | Functions to assess RNA Degradation. |
| xpsSummarize | Probe Set Summarizing Functions |
| xpsSummarize-method | Class DataTreeSet |
| xpsSummarize-methods | Probe Set Summarizing Functions |
| xpsUniFilter | Function for Applying an UniFilter to an ExprTreeSet |
| xpsUniFilter-method | Class ExprTreeSet |
| xpsUniFilter-methods | Function for Applying an UniFilter to an ExprTreeSet |