PAA: an R/bioconductor package for biomarker discovery with protein microarrays

Bioinformatics. 2016 May 15;32(10):1577-9. doi: 10.1093/bioinformatics/btw037. Epub 2016 Jan 22.


The R/Bioconductor package Protein Array Analyzer (PAA) facilitates a flexible analysis of protein microarrays for biomarker discovery (esp., ProtoArrays). It provides a complete data analysis workflow including preprocessing and quality control, uni- and multivariate feature selection as well as several different plots and results tables to outline and evaluate the analysis results. As a main feature, PAA's multivariate feature selection methods are based on recursive feature elimination (e.g. SVM-recursive feature elimination, SVM-RFE) with stability ensuring strategies such as ensemble feature selection. This enables PAA to detect stable and reliable biomarker candidate panels.

Availability and implementation: PAA is freely available (BSD 3-clause license) from CONTACT: or

MeSH terms

  • Biomarkers
  • Protein Array Analysis*
  • Software


  • Biomarkers