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 <email@example.com>, Martin Eisenacher <firstname.lastname@example.org>|
|License||BSD_3_clause + file LICENSE|
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.