PAA-Protein_Array_Analyzer

The software tool "PAA-Protein_Array_Analyzer" is an R package designed for the flexible analysis of protein microarrays, focusing on biomarker discovery, particularly in ProtoArrays. It offers a comprehensive data analysis workflow encompassing preprocessing, quality control, and uni- and multivariate feature selection. The package provides various plots and results tables to present and evaluate analysis outcomes. A notable feature of PAA is its use of multivariate feature selection methods based on recursive feature elimination, such as SVM-recursive feature elimination (SVM-RFE), coupled with stability-ensuring strategies like ensemble feature selection.

Topic

Proteomics;Biomarkers;Microarray experiment

Detail

  • Operation: Differential protein expression analysis

  • Software interface: Command-line user interface,Library

  • Language: R,C++

  • License: The 3-Clause BSD License

  • Cost: Free

  • Version name: 1.36.0

  • Credit: P.U.R.E., a project of Nordrhein-Westfalen, a federal state of Germany, de.NBI, a project of the German Federal Ministry of Education and Research (BMBF).

  • Input: Raw microarray data, Text [TSV]

  • Output: ID list [TSV], Plot [PNG] [tiff]

  • Contact: Michael Turewicz michael.turewicz@rub.de, Martin Eisenacher martin.eisenacher@rub.de

  • Collection: -

  • Maturity: Mature

Publications

  • PAA: an R/bioconductor package for biomarker discovery with protein microarrays.
  • Turewicz M, et al. PAA: an R/bioconductor package for biomarker discovery with protein microarrays. PAA: an R/bioconductor package for biomarker discovery with protein microarrays. 2016; 32:1577-9. doi: 10.1093/bioinformatics/btw037
  • https://doi.org/10.1093/bioinformatics/btw037
  • PMID: 26803161
  • PMC: PMC4866526

Download and documentation

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