PAA: PAA (Protein Array Analyzer)

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PAA")
AuthorMichael Turewicz [aut, cre], Martin Eisenacher [ctb, cre]
Bioconductor views Classification Microarray OneChannel Proteomics
Date of publicationNone
MaintainerMichael Turewicz <michael.turewicz@rub.de>, Martin Eisenacher <martin.eisenacher@rub.de>
LicenseBSD_3_clause + file LICENSE
Version1.10.0
http://www.ruhr-uni-bochum.de/mpc/software/PAA/

View on Bioconductor

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/PAA.r R/RcppExports.R
README
build
build/vignette.rds
demo
demo/00Index
demo/example.r
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/PAA_1.7.1.pdf
inst/doc/PAA_vignette.R
inst/doc/PAA_vignette.Rnw
inst/doc/PAA_vignette.pdf
inst/extdata
inst/extdata/Alzheimer.RData
inst/extdata/AlzheimerControls.RData
inst/extdata/BadData.RData
inst/extdata/DummyData.RData
inst/extdata/data_info.txt
inst/extdata/dummy_GSM734833_PA41992_-_AD1.gpr
inst/extdata/dummy_GSM734833_PA41992_-_AD1_no_descr.gpr
inst/extdata/dummy_GSM734834_PA41994_-_AD2.gpr
inst/extdata/dummy_GSM734835_PA42006_-AD3.gpr
inst/extdata/dummy_GSM734836_PA42005_-_AD4.gpr
inst/extdata/dummy_GSM734837_PA41957_-_AD5.gpr
inst/extdata/dummy_GSM735203_PA42023_-_CO13.gpr
inst/extdata/dummy_GSM735203_PA42023_-_CO13_no_descr.gpr
inst/extdata/dummy_GSM735204_PA42025_-_CO14.gpr
inst/extdata/dummy_GSM735205_PA42026_-_CO15.gpr
inst/extdata/dummy_GSM735206_PA42028_-_CO16.gpr
inst/extdata/dummy_GSM735207_PA42029_-_CO17.gpr
inst/extdata/dummy_no_descr_targets.txt
inst/extdata/dummy_targets_AD&NDC.txt
inst/extdata/selectFeaturesResultsEns.RData
inst/extdata/selectFeaturesResultsFreq.RData
inst/extdata/targets_AD&NDC.txt
inst/unitTests
inst/unitTests/test_batchAdjust.R inst/unitTests/test_batchFilter.R inst/unitTests/test_diffAnalysis.R inst/unitTests/test_loadGPR.R inst/unitTests/test_normalizeArrays.R inst/unitTests/test_preselect.r inst/unitTests/test_printFeatures.R
man
man/batchAdjust.Rd man/batchFilter.Rd man/batchFilter.anova.Rd man/diffAnalysis.Rd man/loadGPR.Rd man/mMsMatrix.Rd man/normalizeArrays.Rd man/plotArray.Rd man/plotFeatures.Rd man/plotFeaturesHeatmap.2.Rd man/plotFeaturesHeatmap.Rd man/plotMAPlots.Rd man/plotNormMethods.Rd man/preselect.Rd man/printFeatures.Rd man/pvaluePlot.Rd man/selectFeatures.Rd
man/shuffleData.rd
man/volcanoPlot.Rd
src
src/Makevars
src/Makevars.win
src/PAA_init.c
src/RcppExports.cpp
src/joinMCountResults.cpp
src/mCount.cpp
src/mMsMatrix.cpp
src/sampling.cpp
tests
tests/runTests.R
vignettes
vignettes/PAA_vignette.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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