# Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

## Documentation for package ‘RPPanalyzer’ version 1.4.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

RPPanalyzer-package | Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact.
analyzeIntercepts | Dilution series intersect correction
as.my | Dilution series intersect correction
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.
getIntercepts | Dilution series intersect correction
getSignals | Dilution series intersect correction
HKdata | Reverse phase protein array data of siRNA transfected cell line
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
plotqq | qq-plot and qq-line of an RPPA data set
plotTimeCourse | Draw time course from RPPA data
plotTimeCourseII | Multiplot function for RPPA time course datasets
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
RPPanalyzer | 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
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