PAA: PAA (Protein Array Analyzer)

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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.

Author
Michael Turewicz [aut, cre], Martin Eisenacher [ctb, cre]
Date of publication
None
Maintainer
Michael Turewicz <michael.turewicz@rub.de>, Martin Eisenacher <martin.eisenacher@rub.de>
License
BSD_3_clause + file LICENSE
Version
1.8.0
URLs

View on Bioconductor

Man pages

batchAdjust
Adjust microarray data for batch effects.
batchFilter
Remove differential features regarding array batches/lots.
batchFilter.anova
Remove features which are differential regarding microarray...
diffAnalysis
Differential analysis.
loadGPR
Importing raw data from gpr files.
mMsMatrix
Compute a reference minimum M statistic (n1 x n2)-matrix.
normalizeArrays
Normalize microarray data.
plotArray
Plot ProtoArray expression intensities in the original...
plotFeatures
Plot intensities of features.
plotFeaturesHeatmap
Plot feature intensities as a heatmap.
plotFeaturesHeatmap.2
Alternative function to plot feature intensities as a...
plotMAPlots
Check normalization results with MA plots.
plotNormMethods
Check normalization results with boxplots.
preselect
Score and preselect features.
printFeatures
Print features into a table.
pvaluePlot
Draw a p-value plot.
selectFeatures
Select features using frequency-based or ensemble feature...
volcanoPlot
Draw a volcano plot.

Files in this package

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