two-colour cDNA array quality control and preprocessing


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Documentation for package `arrayMagic' version 1.8.0

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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)