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RPPanalyzer (version 1.3)

Reads, annotates, and normalizes reverse phase protein array data

Description

Reads in sample description and slide description files and annotates the expression values taken from gpr files. After normalization data can be visualized as boxplot, heatmap or dotplot.

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Version

Install

install.packages('RPPanalyzer')

Monthly Downloads

248

Version

1.3

License

LGPL

Maintainer

Christian Bender

Last Published

June 29th, 2014

Functions in RPPanalyzer (1.3)

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.
rppaList2Heatmap

Draw a heatmap with column side colors from a RPPA data
plotMeasurementsQC

Scatter Plots from an RPPA data
dataIII

Reverse phase protein array data from original cancer specimen
calcLogistic

Calculates sample concentrations using sigmoid model fit
normalizeRPPA

Normalizes data in an RPPA data list
pick.high.conc

Select the highest concentration from serialy diluted samples
sampledescription.old

sample description file
S1.gpr

GenePix result files
remove.arrays

Remove arrays from a RPPA data list
curvePredictSigmoid

Sigmoidal curve prediction.
select.measurements

Selects the measurement samples from an RPPA data list
rppa2boxplot

Draws boxplots of groups of an RPPA data set including wilcox or kruskal test.
calcLinear

Calculates sample concentrations using linear model fit
write.Data

writes an RPPA data list into csv file
dataI

Reverse phase protein array rawdata, samples serially diluted
sample.median

Aggregate the replicates in an RPPA data set
averageData

Average biological replicates over different slides.
calcSdc

Calculates the concentration of serial diluted samples
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.
plotqq

qq-plot and qq-line of an RPPA data set
dataII

Reverse phase protein array data, samples from a stimulation time course
ser.dil.samples

Reverse phase protein array rawdata, samples serially diluted
correctDilinterc

Dilution series intersect correction
plotTimeCourseII

Multiplot function for RPPA time course datasets
plotQC

Plot target and blank signal from RPPA control samples
rppaList2ExpressionSet

Convert RPPA data into Expression Set
plotTimeCourse

Draw time course from RPPA data
test.correlation

Tests for correlations in RPPA data
simpleBoxplot

Draws boxplots of groups of an RPPA data set.
slidedescription.old

slide description file
sampledescription.txt

sample description file
correctBG

Corrects for background in an RPPA data set
select.sample.group

Selects samples from RPPA data
logList

Logarithmize (log2) the first two RPPA list elements, i.e. foreground and background signal intensities
read.Data

Read and Annotate RPPA rawdata
slidedescription.txt

slide description file
dataPreproc

Data preprocessing