| addData |
Import additional CEL files into a DataTreeSet |
| addData,DataTreeSet-method |
Class DataTreeSet |
| addData-methods |
Import additional CEL files into a DataTreeSet |
| AnalysisTreeSet |
Class AnalysisTreeSet |
| AnalysisTreeSet-class |
Class AnalysisTreeSet |
| arrayInfo |
Class ProjectInfo |
| arrayInfo,ProjectInfo-method |
Class ProjectInfo |
| arrayInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
| attachBgrd |
Attach/Remove Background Intensities |
| attachBgrd,DataTreeSet-method |
Class DataTreeSet |
| attachBgrd-methods |
Attach/Remove Background Intensities |
| attachInten |
Attach/Remove Intensities |
| attachInten,DataTreeSet-method |
Class DataTreeSet |
| attachInten-methods |
Attach/Remove Intensities |
| attachMask |
Attach/Remove Scheme Mask |
| attachMask,DataTreeSet-method |
Class DataTreeSet |
| attachMask,SchemeTreeSet-method |
Class SchemeTreeSet |
| attachMask-methods |
Attach/Remove Scheme Mask |
| authorInfo |
Class ProjectInfo |
| authorInfo,ProjectInfo-method |
Class ProjectInfo |
| authorInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
| callFilter |
Detection Call Filter |
| callFilter,PreFilter-method |
Class PreFilter |
| callFilter,UniFilter-method |
Class UniFilter |
| callFilter-methods |
Detection Call Filter |
| callFilter<-,PreFilter,character-method |
Class PreFilter |
| callFilter<-,UniFilter,character-method |
Class UniFilter |
| callplot |
Barplot of Percent Present and Absent Calls. |
| callplot,CallTreeSet-method |
Class CallTreeSet |
| callplot-methods |
Barplot of Percent Present and Absent Calls. |
| CallTreeSet |
Class CallTreeSet |
| callTreeset |
Class FilterTreeSet |
| callTreeset,FilterTreeSet-method |
Class FilterTreeSet |
| CallTreeSet-class |
Class CallTreeSet |
| cellineInfo |
Class ProjectInfo |
| cellineInfo,ProjectInfo-method |
Class ProjectInfo |
| cellineInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
| chipMask |
Class SchemeTreeSet |
| chipMask,SchemeTreeSet-method |
Class SchemeTreeSet |
| chipMask<-,SchemeTreeSet,data.frame-method |
Class SchemeTreeSet |
| chipName |
Class SchemeTreeSet |
| chipName,ProcesSet-method |
Class ProcesSet |
| chipName,SchemeTreeSet-method |
Class SchemeTreeSet |
| chipType |
Class SchemeTreeSet |
| chipType,ProcesSet-method |
Class ProcesSet |
| chipType,SchemeTreeSet-method |
Class SchemeTreeSet |
| chipType<-,SchemeTreeSet,character-method |
Class SchemeTreeSet |
| cvFilter |
Coefficient of Variation Filter |
| cvFilter,PreFilter-method |
Class PreFilter |
| cvFilter-methods |
Coefficient of Variation Filter |
| cvFilter<-,PreFilter,numeric-method |
Class PreFilter |
| existsROOTFile |
Test for Existing ROOT File |
| export |
Export data as text files |
| export,ProcesSet-method |
Class ProcesSet |
| export,SchemeTreeSet-method |
Class SchemeTreeSet |
| export,TreeSet-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 |
Class ExprTreeSet |
| exprs,ExprTreeSet-method |
Class ExprTreeSet |
| exprs<-,ExprTreeSet,data.frame-method |
Class ExprTreeSet |
| ExprTreeSet |
Class ExprTreeSet |
| exprTreeset |
Class FilterTreeSet |
| exprTreeset,FilterTreeSet-method |
Class FilterTreeSet |
| ExprTreeSet-class |
Class ExprTreeSet |
| exprType |
Class ExprTreeSet |
| exprType,ExprTreeSet-method |
Class ExprTreeSet |
| exprType<-,ExprTreeSet,character-method |
Class ExprTreeSet |
| image |
Display an Image |
| image,DataTreeSet-method |
Class DataTreeSet |
| image-methods |
Display an Image |
| image.dev |
Image for Device |
| 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 |
| initialize |
Initialize Classes |
| initialize,AnalysisTreeSet-method |
Initialize Classes |
| initialize,CallTreeSet-method |
Initialize Classes |
| initialize,DataTreeSet-method |
Initialize Classes |
| initialize,ExprTreeSet-method |
Initialize Classes |
| initialize,Filter-method |
Initialize Classes |
| initialize,FilterTreeSet-method |
Initialize Classes |
| initialize,PreFilter-method |
Initialize Classes |
| initialize,ProcesSet-method |
Initialize Classes |
| initialize,ProjectInfo-method |
Initialize Classes |
| initialize,SchemeTreeSet-method |
Initialize Classes |
| initialize,TreeSet-method |
Initialize Classes |
| initialize,UniFilter-method |
Initialize Classes |
| initialize-methods |
Initialize Classes |
| intensity |
Class DataTreeSet |
| intensity,DataTreeSet-method |
Class DataTreeSet |
| intensity<-,DataTreeSet,data.frame-method |
Class DataTreeSet |
| isROOTFile |
Test for ROOT File |
| pm |
Methods for accessing perfect matches and mismatches |
| pm,DataTreeSet-method |
Class DataTreeSet |
| pm-methods |
Methods for accessing perfect matches and mismatches |
| pmplot |
Barplot of PM and MM Intensities. |
| pmplot,DataTreeSet-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 |
Class CallTreeSet |
| presCall,CallTreeSet-method |
Class CallTreeSet |
| presCall<-,CallTreeSet,data.frame-method |
Class CallTreeSet |
| primcellInfo |
Class ProjectInfo |
| primcellInfo,ProjectInfo-method |
Class ProjectInfo |
| primcellInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
| probeInfo |
Class SchemeTreeSet |
| probeInfo,SchemeTreeSet-method |
Class SchemeTreeSet |
| ProcesSet |
Class ProcesSet |
| ProcesSet-class |
Class ProcesSet |
| ProjectInfo |
Constructor for Class ProjectInfo |
| projectInfo |
Class ProjectInfo |
| projectInfo,DataTreeSet-method |
Class DataTreeSet |
| projectInfo,ProjectInfo-method |
Class ProjectInfo |
| ProjectInfo-class |
Class ProjectInfo |
| projectInfo<-,DataTreeSet,ProjectInfo-method |
Class DataTreeSet |
| projectInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
| pvalData |
Class CallTreeSet |
| pvalData,CallTreeSet-method |
Class CallTreeSet |
| pvalData<-,CallTreeSet,data.frame-method |
Class CallTreeSet |
| ratioFilter |
Ratio Filter |
| ratioFilter,PreFilter-method |
Class PreFilter |
| ratioFilter-methods |
Ratio Filter |
| ratioFilter<-,PreFilter,numeric-method |
Class PreFilter |
| rawCELName |
Method for getting names of the raw CEL-files |
| rawCELName,DataTreeSet-method |
Class DataTreeSet |
| rawCELName-methods |
Method for getting names of the raw CEL-files |
| removeBgrd |
Attach/Remove Background Intensities |
| removeBgrd,DataTreeSet-method |
Class DataTreeSet |
| removeBgrd-methods |
Attach/Remove Background Intensities |
| removeInten |
Attach/Remove Intensities |
| removeInten,DataTreeSet-method |
Class DataTreeSet |
| removeInten-methods |
Attach/Remove Intensities |
| removeMask |
Attach/Remove Scheme Mask |
| removeMask,DataTreeSet-method |
Class DataTreeSet |
| removeMask,SchemeTreeSet-method |
Class SchemeTreeSet |
| removeMask-methods |
Attach/Remove Scheme Mask |
| rma |
Robust Multi-Array Average Expression Measure |
| ROOT |
ROOT An Object-Oriented Data Analysis Framework |
| root.browser |
Open the ROOT object browser |
| root.browser,TreeSet-method |
Class TreeSet |
| root.data |
Create class DataTreeSet accessing ROOT data file |
| root.density |
ROOT Density Plot |
| 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.mvaplot |
ROOT M vs A Plot |
| root.scheme |
Create class SchemeTreeSet accessing ROOT scheme file |
| rootFile |
Class TreeSet |
| rootFile,TreeSet-method |
Class TreeSet |
| rootFile<-,TreeSet,character-method |
Class TreeSet |
| sampleInfo |
Class ProjectInfo |
| sampleInfo,ProjectInfo-method |
Class ProjectInfo |
| sampleInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
| schemeFile |
Class ProcesSet |
| schemeFile,ProcesSet-method |
Class ProcesSet |
| schemeFile<-,ProcesSet,character-method |
Class ProcesSet |
| schemeSet |
Class ProcesSet |
| schemeSet,ProcesSet-method |
Class ProcesSet |
| schemeSet<-,ProcesSet,SchemeTreeSet-method |
Class ProcesSet |
| SchemeTreeSet |
Class SchemeTreeSet |
| SchemeTreeSet-class |
Class SchemeTreeSet |
| se.exprs |
Class ExprTreeSet |
| se.exprs,ExprTreeSet-method |
Class ExprTreeSet |
| setName |
Class TreeSet |
| setName,TreeSet-method |
Class TreeSet |
| setName<-,TreeSet,character-method |
Class TreeSet |
| setType |
Class TreeSet |
| setType,TreeSet-method |
Class TreeSet |
| setType<-,TreeSet,character-method |
Class TreeSet |
| show,ProjectInfo-method |
Class ProjectInfo |
| sourceInfo |
Class ProjectInfo |
| sourceInfo,ProjectInfo-method |
Class ProjectInfo |
| sourceInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
| summarize |
Probe Set Summarizing Functions |
| xps |
xps Package Overview |
| xpsBgCorrect |
Background Correction |
| xpsBgCorrect,DataTreeSet-method |
Class DataTreeSet |
| xpsBgCorrect-methods |
Background Correction |
| xpsDABGCall |
Detection Above Background Call |
| xpsDABGCall,DataTreeSet-method |
Class DataTreeSet |
| xpsDABGCall-methods |
Detection Above Background Call |
| xpsMAS4 |
MAS 4.0 Expression Measure |
| xpsMAS4,DataTreeSet-method |
Class DataTreeSet |
| xpsMAS4-methods |
MAS 4.0 Expression Measure |
| xpsMAS5 |
MAS 5.0 Expression Measure |
| xpsMAS5,DataTreeSet-method |
Class DataTreeSet |
| xpsMAS5-methods |
MAS 5.0 Expression Measure |
| xpsMAS5Call |
MAS 5.0 Absolute Detection Call |
| xpsMAS5Call,DataTreeSet-method |
Class DataTreeSet |
| xpsMAS5Call-methods |
MAS 5.0 Absolute Detection Call |
| xpsNormalize |
Normalization on Affymetrix Probe Level Data or on Expression Levels |
| xpsNormalize,DataTreeSet-method |
Class DataTreeSet |
| xpsNormalize,ExprTreeSet-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,ExprTreeSet-method |
Class ExprTreeSet |
| xpsPreFilter-methods |
Function for Applying a PreFilter to an ExprTreeSet |
| xpsPreprocess |
Compute expression levels from raw data |
| xpsPreprocess,DataTreeSet-method |
Class DataTreeSet |
| xpsPreprocess-methods |
Compute expression levels from raw data |
| xpsRMA |
Robust Multi-Array Average Expression Measure |
| xpsRMA,DataTreeSet-method |
Class DataTreeSet |
| xpsRMA-methods |
Robust Multi-Array Average Expression Measure |
| xpsSummarize |
Probe Set Summarizing Functions |
| xpsSummarize,DataTreeSet-method |
Class DataTreeSet |
| xpsSummarize-methods |
Probe Set Summarizing Functions |
| xpsUniFilter |
Function for Applying an UniFilter to an ExprTreeSet |
| xpsUniFilter,ExprTreeSet-method |
Class ExprTreeSet |
| xpsUniFilter-methods |
Function for Applying an UniFilter to an ExprTreeSet |