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| arrayData | Class arrayData, a simple container for raw data and related information |
| arrayData-class | Class arrayData, a simple container for raw data and related information |
| as.exprSet | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| as.exprSet,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| as.RGList | Class arrayData, a simple container for raw data and related information |
| as.RGList,arrayData-method | Class arrayData, a simple container for raw data and related information |
| as.RGList,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| cbind.arrayData | Cbind for objects of class arrayData |
| cbind.exprSetRG | Cbind for objects of class exprSetRG |
| colCors | Correlation coefficients between the corresponding columns (rows) of two matrices that have the same size. |
| controlledApply | controlledApply |
| controlledSubsetting | Subsetting of Arrays |
| detectReplicas | detectReplicas |
| exprSetRG | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| exprSetRG-class | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| fdc | FDC (false discovery count) |
| getExprSetGreen | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetGreen,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetGreenMinusRed | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetGreenMinusRed,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetLogRatio | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetLogRatio,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetRed | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetRed,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetRedMinusGreen | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getExprSetRedMinusGreen,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getHybAttr | Class arrayData, a simple container for raw data and related information |
| getHybAttr,arrayData-method | Class arrayData, a simple container for raw data and related information |
| getHybAttrGreen | Class arrayData, a simple container for raw data and related information |
| getHybAttrGreen,arrayData-method | Class arrayData, a simple container for raw data and related information |
| getHybAttrList | Class arrayData, a simple container for raw data and related information |
| getHybAttrList,arrayData-method | Class arrayData, a simple container for raw data and related information |
| getHybAttrRed | Class arrayData, a simple container for raw data and related information |
| getHybAttrRed,arrayData-method | Class arrayData, a simple container for raw data and related information |
| getIndGreen | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getIndGreen,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getIndRed | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getIndRed,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| getIntensities | Class arrayData, a simple container for raw data and related information |
| getIntensities,arrayData-method | Class arrayData, a simple container for raw data and related information |
| getSpotAttr | Class arrayData, a simple container for raw data and related information |
| getSpotAttr,arrayData-method | Class arrayData, a simple container for raw data and related information |
| getWeights | Class arrayData, a simple container for raw data and related information |
| getWeights,arrayData-method | Class arrayData, a simple container for raw data and related information |
| hybAttrList<-,arrayData-method | Class arrayData, a simple container for raw data and related information |
| initialize,arrayData-method | Class arrayData, a simple container for raw data and related information |
| initialize,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| intensities<-,arrayData-method | Class arrayData, a simple container for raw data and related information |
| interweave | interweave |
| normalise | Normalisation of microarray data |
| pDataGreen | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| pDataGreen,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| pDataRed | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| pDataRed,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| pDataSlide | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| pDataSlide,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| phenoDataGreen | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| phenoDataGreen,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| phenoDataRed | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| phenoDataRed,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| phenoDataSlide | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| phenoDataSlide,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| plot.imageMatrix | Visualisation of a matrix |
| plotDistributions | Visualisation of distributions |
| processArrayData | Automated processing of two colour DNA microarray data |
| processArrayDataObject | Automated processing and normalisation of an arrayData-object (part of function processArrayData) |
| qualityDiagnostics | Generates quality diagnostic plots |
| qualityParameters | Calculation of quality characteristics for DNA microarray hybridisations |
| readIntensities | readIntensities |
| readpDataSlides | Reads the description of all slides or channels |
| removeSpots | Remove specified spots from objects |
| rowCors | Correlation coefficients between the corresponding columns (rows) of two matrices that have the same size. |
| show,arrayData-method | Class arrayData, a simple container for raw data and related information |
| show,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| simpleApply | simpleApply |
| slideMerge | Averaging of two colour microarray replicas |
| slideSubset | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| slideSubset,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |
| spatialLayout | Calculation of two dimensional coordinates |
| spotAttr<-,arrayData-method | Class arrayData, a simple container for raw data and related information |
| spotMerge | Averaging of spot replicas |
| visualiseHybridisations | Microarray intensity data are visualised with respect to their spatial layout |
| visualiseQualityParameters | Graphical representation of quality parameters |
| weights<-,arrayData-method | Class arrayData, a simple container for raw data and related information |
| write.htmltable | Write a data frame into an html table within a html page |
| writeToFile | Writes a textual representation of an exprSetRG and/or arrayData object |
| [,arrayData-method | Class arrayData, a simple container for raw data and related information |
| [,exprSetRG-method | Class exprSetRG for two colour DNA microarray data (extension of exprSet) |