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RPPanalyzer (version 1.0.5)

Reads, annotates, and normalizes reverse phase protein array data

Description

Reads in sampledescription and slidedescription files and annotates the expression values taken from gpr files. After Normalization data can be presented in boxplots, heatmaps or dotplots.

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Version

Install

install.packages('RPPanalyzer')

Monthly Downloads

248

Version

1.0.5

License

LGPL

Maintainer

Christian Bender

Last Published

October 3rd, 2012

Functions in RPPanalyzer (1.0.5)

calcLogistic

Calculates sample concentrations using sigmoid model fit
S1.gpr

GenePix result files
calcSuperCurve

Calculates the concentration of serial diluted samples
slidedescription

slide description file
plotMeasurementsQC

Scatter Plots from an RPPA data
sample.median

Aggregate the replicates in an RPPA data set
plotqq

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

Reverse phase protein array data, samples from a stimulation time course
plotTimeCourse

Draw time course from RPPA data
calcLinear

Calculates sample concentrations using linear model fit
dataIII

Reverse phase protein array data from original cancer specimen
pick.high.conc

Select the highest concentration from serialy diluted samples
ser.dil.samples

Reverse phase protein array rawdata, samples serially diluted
test.correlation

Tests for correlations in RPPA data
select.measurements

Selects the measurement samples from an RPPA data list
rppaList2Heatmap

Draw a heatmap with column side colors from a RPPA data
rppaList2ExpressionSet

Convert RPPA data into Expression Set
sampledescription.txt

sample description file
dataI

Reverse phase protein array rawdata, samples serially diluted
sampledescription

sample description file
remove.arrays

Remove arrays from a RPPA data list
rppa2boxplot

Draw boxplots of an RPPA data set.
correctBG

Corrects for background in an RPPA data set
read.Data

Read and Annotate RPPA rawdata
write.Data

writes an RPPA data list into csv file
calcSdc

Calculates the concentration of serial diluted samples
slidedescription.txt

slide description file
select.sample.group

Selects samples from RPPA data
normalizeRPPA

Normalizes data in an RPPA data list
plotQC

Plot target and blank signal from RPPA control samples
RPPanalyzer-package

Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact.
HKdata

Reverse phase protein array data of siRNA transfected cell line