title: PAA: an R/bioconductor package for biomarker discovery with protein microarrays.
abstract: 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.
  
  
  
  PAA is freely available (BSD 3-clause license) from http://www.bioconductor.org/packages/PAA/ CONTACT: michael.turewicz@rub.de or martin.eisenacher@rub.de.
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, 44801, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Turewicz
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, 44801, Germany.
authors.forename: Maike
authors.initials: M
authors.lastname: Ahrens
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, 44801, Germany.
authors.forename: Caroline
authors.initials: C
authors.lastname: May
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, 44801, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Marcus
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, 44801, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
mesh_terms: D015415:Biomarkers; D040081:Protein Array Analysis; D012984:Software
chemical_list: D015415:Biomarkers