# PAA (Protein Array Analyzer)

## Documentation for package ‘PAA’ version 1.20.0

- 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.