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This is the development version of PAA; for the stable release version, see PAA.

PAA (Protein Array Analyzer)

Bioconductor version: Development (3.19)

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]

Maintainer: Michael Turewicz <michael.turewicz at>, Martin Eisenacher <martin.eisenacher at>

Citation (from within R, enter citation("PAA")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews Classification, Microarray, OneChannel, Proteomics, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License BSD_3_clause + file LICENSE
Depends R (>= 3.2.0), Rcpp (>= 0.11.6)
Imports e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva
System Requirements C++ software package Random Jungle
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Suggests BiocStyle, RUnit, BiocGenerics, vsn
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