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R/DWD: Distance-weighted Discrimination for Classification, Visualization and Batch Adjustment

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2012 Feb 28
PMID 22368246
Citations 21
Authors
Hanwen Huang
Xiaosun Lu
Yufeng Liu
Perry Haaland
J S Marron
Affiliations
Soon will be listed here.
Abstract

Unlabelled: R/DWD is an extensible package for classification. It is built based on a recently developed powerful classification method called distance weighted discrimination (DWD). DWD is related to, and has been shown to be superior to, the support vector machine in situations that are fundamental to bioinformatics, such as very high dimensional data. DWD has proven to be very useful for several fundamental bioinformatics tasks, including classification, data visualization and removal of biases, such as batch effects. Earlier DWD implementations, however, relied on Matlab, which is not free and requires a license. The major contribution of the R/DWD package is an implementation that is completely in R and thus can be used without any requirements for licensing or software purchase. In addition, R/DWD also provides efficient solvers for second-order-cone-programming and quadratic programming.

Availability And Implementation: The package is freely available from cran.r-project.org.

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References
1.
Qiao X, Zhang H, Liu Y, Todd M, Marron J . Weighted Distance Weighted Discrimination and Its Asymptotic Properties. J Am Stat Assoc. 2010; 105(489):401-414. PMC: 2996856. DOI: 10.1198/jasa.2010.tm08487. View
2.
Benito M, Parker J, Du Q, Wu J, Xiang D, Perou C . Adjustment of systematic microarray data biases. Bioinformatics. 2003; 20(1):105-14. DOI: 10.1093/bioinformatics/btg385. View
3.
Liu Y, Zhang H, Wu Y . Hard or Soft Classification? Large-margin Unified Machines. J Am Stat Assoc. 2011; 106(493):166-177. PMC: 3233196. DOI: 10.1198/jasa.2011.tm10319. View
4.
Kuo W, Jenssen T, Butte A, Ohno-Machado L, Kohane I . Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002; 18(3):405-12. DOI: 10.1093/bioinformatics/18.3.405. View
5.
Byvatov E, Schneider G . Support vector machine applications in bioinformatics. Appl Bioinformatics. 2004; 2(2):67-77. View