Man pages for xps
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
| addData-methods | Import additional CEL files into a DataTreeSet |
| AffyRNAdeg | Functions to assess RNA Degradation. |
| AnalysisTreeSet-class | Class AnalysisTreeSet |
| attachBgrd-methods | Attach/Remove Background Intensities |
| attachCall-methods | Attach/Remove Detecion Call Measures |
| attachData-methods | Attach/Remove Data |
| attachDataXY-methods | Attach/Remove (X,Y)-Coordinates |
| attachExpr-methods | Attach/Remove Expression Measures |
| attachInten-methods | Attach/Remove Intensities |
| attachMask-methods | Attach/Remove Scheme Mask |
| attachProbe-methods | Attach/Remove Probe Sequence and/or GC Content |
| attachUnitNames-methods | Attach/Remove Unit Names |
| bgcorrect | Background Correction |
| borderplot-methods | Plots of Border Elements |
| boxplot-methods | Box Plots |
| callFilter-methods | Detection Call Filter |
| callplot-methods | Barplot of Percent Present and Absent Calls. |
| CallTreeSet-class | Class CallTreeSet |
| coiplot-methods | Center-Of-Intensity QC Plots |
| corplot-methods | Array-Array Expression Level Correlation Plot |
| cvFilter-methods | Coefficient of Variation Filter |
| dabg.call | Detection Above Background Call |
| DataTreeSet-class | Class DataTreeSet |
| dfw | Distribution Free Weighted Expression Measure |
| diffFilter-methods | Difference Filter |
| existsROOTFile | Test for Existing ROOT File |
| exonLevel | Conversion of Parameter exonlevel to Integer |
| export | Export data as text files |
| export.filter | Export filter data as text files |
| export.root | Export data from ROOT file |
| express | Compute expression levels from raw data |
| exprs-methods | Get/Set Expression Values |
| ExprTreeSet-class | Class ExprTreeSet |
| extenPart | Get Extension of Tree Names |
| farms | Factor Analysis for Robust Microarray Summarization... |
| fcFilter-methods | Fold-Change Filter |
| Filter-class | Base Class Filter |
| FilterTreeSet-class | Class FilterTreeSet |
| 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-methods | Gap Filter |
| 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-methods | Export Tree Data |
| getTreeNames | Get Tree Names |
| highFilter-methods | Upper Threshold Filter |
| hist-methods | Plot Density Estimate |
| 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-methods | Unit Locations |
| ini.call | Informative/Non-Informative Call |
| initialize-methods | Initialize Classes |
| intensity2GCplot-methods | Boxlot of Probe Intensities Stratified by GC Content. |
| intensity-methods | Get/Set Data Values |
| isROOTFile | Test for ROOT File |
| lowFilter-methods | Lower Threshold Filter |
| madFilter-methods | Median Absolute Deviation Filter |
| 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-methods | Box Plots of Relative M Values |
| metaProbesets | Create MetaProbeset File for APT |
| mvaplot-methods | M vs A Plot |
| namePart | Get Tree Names w/o Extension |
| normalize | Normalization on Affymetrix Probe Level Data or on Expression... |
| NUSE | Normalized Unscaled Standard Errors (NUSE) |
| nuseplot-methods | Box Plots of Normalized Unscaled Standard Errors (NUSE) |
| pcaplot-methods | PCA Plot |
| 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... |
| 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... |
| 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 | Methods for accessing perfect matches and mismatches |
| pmplot-methods | Barplot of PM and MM Intensities. |
| prefilter | Function for Applying a PreFilter to an ExprTreeSet |
| PreFilter-class | Class PreFilter |
| PreFilter-constructor | Constructor for Class PreFilter |
| presCall-methods | Get/Set Present Call Values |
| probeContentGC-methods | Get G/C Content for Probes |
| probeSequence-methods | Get Probe Sequence |
| probesetID2unitID-methods | Conversion between Probeset IDs and UnitIDs |
| probesetplot-methods | Plot of Probe Intensities for a Probeset. |
| ProcesSet-class | Class ProcesSet |
| ProjectInfo-class | Class ProjectInfo |
| ProjectInfo-constructor | Constructor for Class ProjectInfo |
| qualify | Probe Set Quality Control Functions |
| QualTreeSet-class | Class QualTreeSet |
| quantileFilter-methods | Quantile Filter |
| ratioFilter-methods | Ratio Filter |
| rawCELName-methods | Method for getting names of the raw CEL-files |
| RLE | Relative Log Expression (RLE) |
| rleplot-methods | Box Plots of Relative Log Expression (RLE) |
| rma | Robust Multi-Array Average Expression Measure |
| ROOT | ROOT An Object-Oriented Data Analysis Framework |
| root.browser-methods | Open the ROOT object browser |
| 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 |
| SchemeTreeSet-class | Class SchemeTreeSet |
| summarize | Probe Set Summarizing Functions |
| symbol2unitID-methods | Conversion between Gene Symbols and UnitIDs |
| treeInfo-methods | Get UserInfo from ROOT Trees |
| TreeSet-class | Class TreeSet |
| trma | transposed Robust Multi-Array Average Expression Measure |
| type2Exten | Convert Method Type to Tree Extension |
| unifilter | Function for Applying an UniFilter to an ExprTreeSet |
| UniFilter-class | Class UniFilter |
| UniFilter-constructor | Constructor for Class UniFilter |
| unitestFilter-methods | Unitest Filter |
| uniTest-methods | A Two-Group Unitest |
| validCall-methods | Get Valid Detection Call Values |
| validData-methods | Extract Subset of Data |
| validExpr-methods | Get Valid Expression Levels |
| validSE-methods | Get Valid Standard Errors |
| validTreetype | Validate Tree Type |
| varFilter-methods | Variance Filter |
| volcanoplot-methods | Volcano Plot |
| xpsOptions | xps Options |
| xps-package | xps Package Overview |
| xpsQAReport | Create Quality Assessment Report. |
