Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

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Documentation for package ‘RPPanalyzer’ version 1.4.8

• 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