Abstract Summary: Data Analysis Tool Extension (DAnTE) is a statistical tool designed to address challenges associated with quantitative bottom-up, shotgun proteomics data. This tool has also been demonstrated for microarray data and can easily be extended to other high-throughput data types. DAnTE features selected normalization methods, missing value imputation algorithms, peptide-to-protein rollup methods, an extensive array of plotting functions and a comprehensive hypothesis-testing scheme that can handle unbalanced data and random effects. The graphical user interface (GUI) is designed to be very intuitive and user friendly. Availability: DAnTE may be downloaded free of charge at http://omics.pnl.gov/software/ Contact: rds@pnl.gov or proteomics@pnl.gov Supplementary information: An example dataset with instructions on how to perform a series of analysis steps is available at http://omics.pnl.gov/software/

DAnTE: a statistical tool for quantitative analysis of -omics data