Protein Array Analyzer (PAA) is a R/Bioconductor package for protein microarray data analysis (esp., ProtoArray data) for biomarker discovery. It imports single color (protein) microarray data that has been saved in gpr file format and can be extended easily to further data formats and technologies. After pre-processing (background correction, batch filtering, normalization) univariate feature pre-selection is performed (e.g., using the "minimum M statistic" approach). 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. PAA is addressed to expert data analysts and developers.
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Funding: Service provision and maintenance funded by de.NBI.