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RPPanalyzer (version 1.0.4)

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

1.0.4

License

LGPL

Maintainer

Heiko Mannsperger

Last Published

August 2nd, 2011

Functions in RPPanalyzer (1.0.4)

calcSuperCurve

Calculates the concentration of serial diluted samples
correctBG

Corrects for background in an RPPA data set
calcLogistic

Calculates sample concentrations using sigmoid model fit
S1.gpr

GenePix result files
calcLinear

Calculates sample concentrations using linear model fit
pick.high.conc

Select the highest concentration from serialy diluted samples
dataI

Reverse phase protein array rawdata, samples serially diluted
dataIII

Reverse phase protein array data from original cancer specimen
select.measurements

Selects the measurement samples from an RPPA data list
read.Data

Read and Annotate RPPA rawdata
sampledescription

sample description file
calcSdc

Calculates the concentration of serial diluted samples
plotqq

qq-plot and qq-line of an RPPA data set
sampledescription.txt

sample description file
rppaList2ExpressionSet

Convert RPPA data into Expression Set
plotMeasurementsQC

Scatter Plots from an RPPA data
ser.dil.samples

Reverse phase protein array rawdata, samples serially diluted
write.Data

writes an RPPA data list into csv file
rppaList2Heatmap

Draw a heatmap with column side colors from a RPPA data
RPPanalyzer-package

Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact.
rppa2boxplot

Draw boxplots of an RPPA data set.
slidedescription.txt

slide description file
sample.median

Aggregate the replicates in an RPPA data set
dataII

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

Draw time course from RPPA data
slidedescription

slide description file
plotQC

Plot target and blank signal from RPPA control samples
remove.arrays

Remove arrays from a RPPA data list
select.sample.group

Selects samples from RPPA data
test.correlation

Tests for correlations in RPPA data
HKdata

Reverse phase protein array data of siRNA transfected cell line
normalizeRPPA

Normalizes data in an RPPA data list