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PAA (version 1.7.1)

PAA (Protein Array Analyzer)

Description

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.

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Version

Version

1.7.1

License

BSD_3_clause + file LICENSE

Maintainer

Michael Turewicz

Last Published

February 15th, 2017

Functions in PAA (1.7.1)

batchFilter.anova

Remove features which are differential regarding microarray batches / lots in a multi-batch scenario.

Print features into a table.

Plot intensities of features.

Adjust microarray data for batch effects.

Differential analysis.

Compute a reference minimum M statistic (n1 x n2)-matrix.

plotNormMethods

Check normalization results with boxplots.

Shuffles class labels to obtain random groups.

Remove differential features regarding array batches/lots.

Plot ProtoArray expression intensities in the original arrangement mimicking the original scan image.

Select features using frequency-based or ensemble feature selection.

normalizeArrays

Normalize microarray data.

Check normalization results with MA plots.

Draw a p-value plot.

Draw a volcano plot.

plotFeaturesHeatmap

Plot feature intensities as a heatmap.

Importing raw data from gpr files.

Score and preselect features.

plotFeaturesHeatmap.2

Alternative function to plot feature intensities as a heatmap.