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Bioinformatics Advance Access published online on May 3, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn217
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Ashoka D. Polpitiya , Wei-Jun Qian , Navdeep Jaitly , Vladislav A. Petyuk , Joshua N. Adkins , David G. Camp, II , Gordon A. Anderson and Richard D. Smith *

Pacific Northwest National Laboratory, Richland, WA 99352, USA.

*To whom correspondence should be addressed. Dr. Richard D. Smith, E-mail: rds{at}pnl.gov or proteomics{at}pnl.gov


  Abstract

Summary: DAnTE (Data Analysis Tool Extension) 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://ncrr.pnl.gov/software/

Contact: rds{at}pnl.gov or proteomics{at}pnl.gov

Supplementary information: An example dataset with instructions on how to perform a series of analysis steps is available at http://ncrr.pnl.gov/software/

Associate Editor: Prof. John Quackenbush

Received on February 22, 2008; revised on April 9, 2008; accepted on April 29, 2008

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