PAA: an R/bioconductor package for biomarker discovery with protein microarrays
M Turewicz, M Ahrens, C May, K Marcus… - …, 2016 - academic.oup.com
M Turewicz, M Ahrens, C May, K Marcus, M Eisenacher
Bioinformatics, 2016•academic.oup.comThe 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 (eg SVM-recursive feature elimination, SVM-RFE) with …
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 (eg SVM-recursive feature elimination, SVM-RFE) with …
Abstract
Summary: 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 http://www.bioconductor.org/packages/PAA/.
Contact: michael.turewicz@rub.de or martin.eisenacher@rub.de
Oxford University Press