RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

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Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.

Author
Heiko Mannsperger with contributions of Stephan Gade
Date of publication
2016-02-11 16:43:06
Maintainer
Astrid Wachter <astrid.wachter@med.uni-goettingen.de>
License
LGPL
Version
1.4.3

View on CRAN

Man pages

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...
dataIII
Reverse phase protein array data from original cancer...
dataPreproc
Data preprocessing
getErrorModel
Estimates error model parameters var0 (basal variance) and...
HKdata
Reverse phase protein array data of siRNA transfected cell...
logList
Logarithmize (log2) the first two RPPA list elements, i.e....
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...
rppaList2ExpressionSet
Convert RPPA data into Expression Set
rppaList2Heatmap
Draw a heatmap with column side colors from a RPPA data
rppanalyzer-package
Read, annotate and normalize reverse phase protein array data...
S1.gpr
GenePix result files
sampledescription.old
sample description file
sampledescription.txt
sample description file
sample.median
Aggregate the replicates in an RPPA data set
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

Files in this package

RPPanalyzer
RPPanalyzer/inst
RPPanalyzer/inst/extdata
RPPanalyzer/inst/extdata/Slide3.gpr
RPPanalyzer/inst/extdata/slidedescription.txt
RPPanalyzer/inst/extdata/S1.gpr
RPPanalyzer/inst/extdata/Slide2.gpr
RPPanalyzer/inst/extdata/Slide1.gpr
RPPanalyzer/inst/extdata/FCF_Slide.gpr
RPPanalyzer/inst/extdata/S4.gpr
RPPanalyzer/inst/extdata/sampledescription.txt
RPPanalyzer/inst/extdata/S2.gpr
RPPanalyzer/inst/doc
RPPanalyzer/inst/doc/RPPanalyzer.R
RPPanalyzer/inst/doc/RPPanalyzer.pdf
RPPanalyzer/inst/doc/RPPanalyzer.rnw
RPPanalyzer/NAMESPACE
RPPanalyzer/data
RPPanalyzer/data/dataII.RData
RPPanalyzer/data/sampledescription.old.txt.gz
RPPanalyzer/data/HKdata.RData
RPPanalyzer/data/dataI.RData
RPPanalyzer/data/dataIII.RData
RPPanalyzer/data/ser.dil.samples.RData
RPPanalyzer/data/slidedescription.old.txt.gz
RPPanalyzer/R
RPPanalyzer/R/rppa2boxplot.R
RPPanalyzer/R/select.measurements.R
RPPanalyzer/R/pick.high.conc.R
RPPanalyzer/R/correctDilinterc.R
RPPanalyzer/R/dataPreproc.R
RPPanalyzer/R/create.ID.col.R
RPPanalyzer/R/plotHeatmap.R
RPPanalyzer/R/array.id.R
RPPanalyzer/R/curvePredictLinear.R
RPPanalyzer/R/annotate.samples.R
RPPanalyzer/R/getErrorModel.R
RPPanalyzer/R/rppaList2Heatmap.R
RPPanalyzer/R/correctBG.R
RPPanalyzer/R/plotTimeCourse.R
RPPanalyzer/R/norm.BCA.R
RPPanalyzer/R/sample.median.R
RPPanalyzer/R/sub.ID.R
RPPanalyzer/R/heatmapcolors.R
RPPanalyzer/R/protein.con.R
RPPanalyzer/R/calcLinear.R
RPPanalyzer/R/samples.id.R
RPPanalyzer/R/rppaList2ExpressionSet.R
RPPanalyzer/R/simpleBoxplot.R
RPPanalyzer/R/spotbyspot.R
RPPanalyzer/R/plotMeasurementsQC.R
RPPanalyzer/R/get.Splines.R
RPPanalyzer/R/remove.arrays.R
RPPanalyzer/R/median.raw.R
RPPanalyzer/R/calcLogistic.R
RPPanalyzer/R/norm.texas.R
RPPanalyzer/R/read.sampledescription.R
RPPanalyzer/R/normalizeRPPA.R
RPPanalyzer/R/annotate.arrays.R
RPPanalyzer/R/test.correlation.R
RPPanalyzer/R/createColumnIndices.R
RPPanalyzer/R/read.Data.R
RPPanalyzer/R/curveFitSigmoid.R
RPPanalyzer/R/norm.static.II.R
RPPanalyzer/R/dil.ser.id.R
RPPanalyzer/R/logList.R
RPPanalyzer/R/curvePredictSigmoid.R
RPPanalyzer/R/g.link.R
RPPanalyzer/R/Sips.R
RPPanalyzer/R/select.sample.group.R
RPPanalyzer/R/read.gpr.R
RPPanalyzer/R/write.Data.R
RPPanalyzer/R/curveFitLinear.R
RPPanalyzer/R/norm.static.I.R
RPPanalyzer/R/calcSdc.R
RPPanalyzer/R/averageData.R
RPPanalyzer/R/read.slidedescription.R
RPPanalyzer/R/plotqq.R
RPPanalyzer/R/plotQC.R
RPPanalyzer/R/slides.id.R
RPPanalyzer/R/plotTimeCourseII.R
RPPanalyzer/R/plotDilutionSeries.R
RPPanalyzer/vignettes
RPPanalyzer/vignettes/workflow_RPPanalyzer.png
RPPanalyzer/vignettes/papers_RPPanalyzer.bib
RPPanalyzer/vignettes/Figure1.png
RPPanalyzer/vignettes/b2-clj4700dn-p2
RPPanalyzer/vignettes/RPPanalyzer.rnw
RPPanalyzer/MD5
RPPanalyzer/build
RPPanalyzer/build/vignette.rds
RPPanalyzer/DESCRIPTION
RPPanalyzer/man
RPPanalyzer/man/logList.Rd
RPPanalyzer/man/sampledescription.txt.Rd
RPPanalyzer/man/rppanalyzer-package.Rd
RPPanalyzer/man/write.Data.Rd
RPPanalyzer/man/pick.high.conc.Rd
RPPanalyzer/man/sample.median.Rd
RPPanalyzer/man/read.Data.Rd
RPPanalyzer/man/remove.arrays.Rd
RPPanalyzer/man/slidedescription.txt.Rd
RPPanalyzer/man/rppaList2ExpressionSet.Rd
RPPanalyzer/man/getErrorModel.Rd
RPPanalyzer/man/dataIII.Rd
RPPanalyzer/man/averageData.Rd
RPPanalyzer/man/correctDilinterc.Rd
RPPanalyzer/man/slidedescription.old.Rd
RPPanalyzer/man/HKdata.Rd
RPPanalyzer/man/plotTimeCourse.Rd
RPPanalyzer/man/correctBG.Rd
RPPanalyzer/man/calcSdc.Rd
RPPanalyzer/man/select.measurements.Rd
RPPanalyzer/man/plotQC.Rd
RPPanalyzer/man/select.sample.group.Rd
RPPanalyzer/man/curvePredictSigmoid.Rd
RPPanalyzer/man/dataII.Rd
RPPanalyzer/man/dataI.Rd
RPPanalyzer/man/calcLogistic.Rd
RPPanalyzer/man/sampledescription.old.Rd
RPPanalyzer/man/dataPreproc.Rd
RPPanalyzer/man/rppa2boxplot.Rd
RPPanalyzer/man/test.correlation.Rd
RPPanalyzer/man/plotTimeCourseII.Rd
RPPanalyzer/man/ser.dil.samples.Rd
RPPanalyzer/man/simpleBoxplot.Rd
RPPanalyzer/man/plotMeasurementsQC.Rd
RPPanalyzer/man/rppaList2Heatmap.Rd
RPPanalyzer/man/plotqq.Rd
RPPanalyzer/man/S1.gpr.Rd
RPPanalyzer/man/calcLinear.Rd
RPPanalyzer/man/normalizeRPPA.Rd