Reads, annotates, and normalizes reverse phase protein array data

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Documentation for package ‘RPPanalyzer’ version 1.0.2

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RPPanalyzer-package Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact.
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
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
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
read.Data Read and Annotate RPPA rawdata
remove.arrays Remove arrays from a RPPA data list
rppa2boxplot Draw boxplots of an RPPA data set.
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.txt sample description file
select.measurements Selects the measurement samples from an RPPA data list
select.sample.group Selects samples from RPPA data
slidedescription.txt slide description file
test.correlation Tests for correlations in RPPA data
write.Data writes an RPPA data list into csv file