PAA (Protein Array Analyzer)

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Documentation for package ‘PAA’ version 1.36.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.
• Package NEWS.

Help 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 batches / lots in a multi-batch scenario.
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 arrangement mimicking the original scan image.
plotFeatures	Plot intensities of features.
plotFeaturesHeatmap	Plot feature intensities as a heatmap.
plotFeaturesHeatmap.2	Alternative function to plot feature intensities as a heatmap.
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 selection.
shuffleData	Shuffles class labels to obtain random groups.
volcanoPlot	Draw a volcano plot.