# two-colour cDNA array quality control and preprocessing

## Documentation for package `arrayMagic' version 1.14.0

## User Guides and Package Vignettes

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## Help Pages

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)