Entry: arrayData-class
Aliases: arrayData-class arrayData intensities<- weights<- spotAttr<- hybAttrList<- getIntensities getWeights getSpotAttr getHybAttr getHybAttrGreen getHybAttrRed getHybAttrList intensities<-,arrayData-method weights<-,arrayData-method spotAttr<-,arrayData-method hybAttrList<-,arrayData-method getIntensities,arrayData-method getWeights,arrayData-method getSpotAttr,arrayData-method getHybAttr,arrayData-method getHybAttrGreen,arrayData-method getHybAttrRed,arrayData-method getHybAttrList,arrayData-method initialize,arrayData-method [,arrayData-method show,arrayData-method
Keywords: methods classes
Description: Class arrayData, a simple container for raw data and related information
URL: ../../../library/arrayMagic/html/arrayData-class.html

Entry: cbind.arrayData
Aliases: cbind.arrayData
Keywords: methods
Description: Cbind for objects of class arrayData
URL: ../../../library/arrayMagic/html/cbind.arrayData.html

Entry: cbind.exprSetRG
Aliases: cbind.exprSetRG
Keywords: methods
Description: Cbind for objects of class exprSetRG
URL: ../../../library/arrayMagic/html/cbind.exprSetRG.html

Entry: colCors
Aliases: rowCors colCors
Keywords: math
Description: Correlation coefficients between the corresponding columns (rows) of two matrices that have the same size.
URL: ../../../library/arrayMagic/html/colCors.html

Entry: controlledApply
Aliases: controlledApply
Keywords: iteration
Description: controlledApply
URL: ../../../library/arrayMagic/html/controlledApply.html

Entry: controlledSubsetting
Aliases: controlledSubsetting
Keywords: utilities
Description: Subsetting of Arrays
URL: ../../../library/arrayMagic/html/controlledSubsetting.html

Entry: detectReplicas
Aliases: detectReplicas
Keywords: utilities
Description: detectReplicas
URL: ../../../library/arrayMagic/html/detectReplicas.html

Entry: exprSetRG-class
Aliases: exprSetRG-class exprSetRG as.exprSet as.RGList getExprSetGreen getExprSetGreenMinusRed getExprSetRedMinusGreen getExprSetRed getExprSetLogRatio getIndGreen getIndRed pDataGreen pDataRed pDataSlide phenoDataGreen phenoDataRed phenoDataSlide slideSubset [,exprSetRG-method as.exprSet,exprSetRG-method as.RGList,exprSetRG-method getExprSetGreen,exprSetRG-method getExprSetGreenMinusRed,exprSetRG-method getExprSetRedMinusGreen,exprSetRG-method getExprSetRed,exprSetRG-method getExprSetLogRatio,exprSetRG-method getIndGreen,exprSetRG-method getIndRed,exprSetRG-method initialize,exprSetRG-method pDataGreen,exprSetRG-method pDataRed,exprSetRG-method pDataSlide,exprSetRG-method phenoDataGreen,exprSetRG-method phenoDataRed,exprSetRG-method phenoDataSlide,exprSetRG-method show,exprSetRG-method slideSubset,exprSetRG-method
Keywords: classes methods
Description: Class exprSetRG for two colour DNA microarray data (extension of exprSet)
URL: ../../../library/arrayMagic/html/exprSetRG-class.html

Entry: fdc
Aliases: fdc
Keywords: math
Description: FDC (false discovery count)
URL: ../../../library/arrayMagic/html/fdc.html

Entry: interweave
Aliases: interweave
Keywords: manip
Description: interweave
URL: ../../../library/arrayMagic/html/interweave.html

Entry: normalise
Aliases: normalise
Keywords: utilities
Description: Normalisation of microarray data
URL: ../../../library/arrayMagic/html/normalise.html

Entry: plot.imageMatrix
Aliases: plot.imageMatrix
Keywords: hplot
Description: Visualisation of a matrix
URL: ../../../library/arrayMagic/html/plot.imageMatrix.html

Entry: plotDistributions
Aliases: plotDistributions
Keywords: hplot
Description: Visualisation of distributions
URL: ../../../library/arrayMagic/html/plotDistributions.html

Entry: processArrayData
Aliases: processArrayData
Keywords: utilities
Description: Automated processing of two colour DNA microarray data
URL: ../../../library/arrayMagic/html/processArrayData.html

Entry: processArrayDataObject
Aliases: processArrayDataObject
Keywords: utilities
Description: Automated processing and normalisation of an arrayData-object (part of function processArrayData)
URL: ../../../library/arrayMagic/html/processArrayDataObject.html

Entry: qualityDiagnostics
Aliases: qualityDiagnostics
Keywords: hplot
Description: Generates quality diagnostic plots
URL: ../../../library/arrayMagic/html/qualityDiagnostics.html

Entry: qualityParameters
Aliases: qualityParameters
Keywords: utilities
Description: Calculation of quality characteristics for DNA microarray hybridisations
URL: ../../../library/arrayMagic/html/qualityParameters.html

Entry: readIntensities
Aliases: readIntensities
Keywords: IO
Description: readIntensities
URL: ../../../library/arrayMagic/html/readIntensities.html

Entry: readpDataSlides
Aliases: readpDataSlides
Keywords: IO
Description: Reads the description of all slides or channels
URL: ../../../library/arrayMagic/html/readpDataSlides.html

Entry: removeSpots
Aliases: removeSpots
Keywords: utilities
Description: Remove specified spots from objects
URL: ../../../library/arrayMagic/html/removeSpots.html

Entry: rowFtests
Aliases: rowFtests rowttests
Keywords: math
Description: F-test and t-test for rows of a matrix
URL: ../../../library/arrayMagic/html/rowFtests.html

Entry: simpleApply
Aliases: simpleApply
Keywords: iteration
Description: simpleApply
URL: ../../../library/arrayMagic/html/simpleApply.html

Entry: slideMerge
Aliases: slideMerge
Keywords: utilities
Description: Averaging of two colour microarray replicas
URL: ../../../library/arrayMagic/html/slideMerge.html

Entry: spatialLayout
Aliases: spatialLayout
Keywords: dplot
Description: Calculation of two dimensional coordinates
URL: ../../../library/arrayMagic/html/spatialLayout.html

Entry: spotMerge
Aliases: spotMerge
Keywords: utilities
Description: Averaging of spot replicas
URL: ../../../library/arrayMagic/html/spotMerge.html

Entry: visualiseHybridisations
Aliases: visualiseHybridisations
Keywords: hplot
Description: Microarray intensity data are visualised with respect to their spatial layout
URL: ../../../library/arrayMagic/html/visualiseHybridisations.html

Entry: visualiseQualityParameters
Aliases: visualiseQualityParameters
Keywords: hplot
Description: Graphical representation of quality parameters
URL: ../../../library/arrayMagic/html/visualiseQualityParameters.html

Entry: write.htmltable
Aliases: write.htmltable
Keywords: IO
Description: Write a data frame into an html table within a html page
URL: ../../../library/arrayMagic/html/write.htmltable.html

Entry: writeToFile
Aliases: writeToFile
Keywords: IO
Description: Writes a textual representation of an exprSetRG and/or arrayData object
URL: ../../../library/arrayMagic/html/writeToFile.html
