HKdata                  Reverse phase protein array data of siRNA
                        transfected cell line
RPPanalyzer-package     Read, annotate and normalize reverse phase
                        protein array data and get a brief overview on
                        the biological impact.
S1.gpr, S2.gpr, S4.gpr
                        GenePix result files
averageData             Average biological replicates over different
                        slides.
calcLinear              Calculates sample concentrations using linear
                        model fit
calcLogistic            Calculates sample concentrations using sigmoid
                        model fit
calcSdc                 Calculates the concentration of serial diluted
                        samples
correctBG               Corrects for background in an RPPA data set
correctDilinterc        Dilution series intersect correction
curvePredictSigmoid     Sigmoidal curve prediction.
dataI                   Reverse phase protein array rawdata, samples
                        serially diluted
dataII                  Reverse phase protein array data, samples from
                        a stimulation time course
dataIII                 Reverse phase protein array data from original
                        cancer specimen
dataPreproc             Data preprocessing
getErrorModel           Estimates error model parameters var0 (basal
                        variance) and varR (relative variance) and
                        produces a new data.frame with the signals and
                        error model parameters.
logList                 Logarithmize (log2) the first two RPPA list
                        elements, i.e. foreground and background signal
                        intensities
normalizeRPPA           Normalizes data in an RPPA data list
pick.high.conc          Select the highest concentration from serialy
                        diluted samples
plotMeasurementsQC      Scatter Plots from an RPPA data
plotQC                  Plot target and blank signal from RPPA control
                        samples
plotTimeCourse          Draw time course from RPPA data
plotTimeCourseII        Multiplot function for RPPA time course
                        datasets
plotqq                  qq-plot and qq-line of an RPPA data set
read.Data               Read and Annotate RPPA rawdata
remove.arrays           Remove arrays from a RPPA data list
rppa2boxplot            Draws boxplots of groups of an RPPA data set
                        including wilcox or kruskal test.
rppaList2ExpressionSet
                        Convert RPPA data into Expression Set
rppaList2Heatmap        Draw a heatmap with column side colors from a
                        RPPA data
sample.median           Aggregate the replicates in an RPPA data set
sampledescription.old   sample description file
sampledescription.txt   sample description file
select.measurements     Selects the measurement samples from an RPPA
                        data list
select.sample.group     Selects samples from RPPA data
ser.dil.samples         Reverse phase protein array rawdata, samples
                        serially diluted
simpleBoxplot           Draws boxplots of groups of an RPPA data set.
slidedescription.old    slide description file
slidedescription.txt    slide description file
test.correlation        Tests for correlations in RPPA data
write.Data              writes an RPPA data list into csv file
