How accurate are the extremely small P-values used in genomic research: An evaluation of numerical libraries

Computational Statistics and Data Analysis

Volumn 53, Issue 7, 2009, Pages 2446-2452

  Santosh Bangalore, Sai ^a   Wang, Jelai ^a   Allison, David B ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE SELECTION AND EVALUATION; LIBRARIES;

CUMULATIVE DISTRIBUTION FUNCTIONS; DATA-SETS; GENOMIC RESEARCHES; GENOMICS; HIGH-DIMENSIONAL; HYPOTHESIS TESTING; JAVA LIBRARIES; MULTIPLE TESTING; NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGIES; NUMERICAL LIBRARIES; OPEN SOURCES; P-VALUES; R FUNCTIONS; SCIENTIFIC SOFTWARES; SIGNIFICANT DIGITS; STATISTICAL DISTRIBUTIONS; STATISTICAL SOFTWARES; T DISTRIBUTIONS;

DISTRIBUTION FUNCTIONS;

EID: 62149117614     PISSN: 01679473     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.csda.2008.11.028     Document Type: Article

References (21)

1. Altman M., Gill J., and McDonald M. Accuracy: Tools for accurate and reliable statistical. Comput. Statist. Data Anal. 21 1 (2007) 1-30
2. Boisvert, R.F., Dongarra, J.J., Pozo, R., Remington, K.A., Stewart, G.W., 1998. Developing numerical libraries in java ACM 1998 workshop on java for high-performance network computing, February 28 and March 1, 1998
3. Brown, B., Lovato, J., Russell, R., 1997. DCDFLIB-Library of C routines for cumulative distribution functions, inverses, and other parameters. Version 1.1. Can be downloaded at (http://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware.asp x?Software_Id=21)
4. 2007. COLT: Open source libraries for high performance scientific and technical computing in java, Lawrence Berkley National Laboratories, Java Documentation Available at (http://dsd.lbl.gov/~hoschek/colt/api/index.html)
5. Cuyt A., Verdonk B., Becuwe S., and Kuterna P. A remarkable example of catastrophic cancellation unraveled. Computing 66 (2001) 309-320
6. GNU Scientific Library, 2007. GSL-GNU Scientific Library, Reference Manual is Available at (http://www.gnu.org/software/gsl/manual/html_node/)
7. Higham N.J. Accuracy and Stability of Numerical Algorithms (1996), Siam pp. 2-61
8. Keeling K.B., and Pavur R.J. A comparative study of the reliability of nine statistical software packages. Comput. Statist. Data Anal. 51 8 (2007) 3811-3831
9. Knusel, L., 2003. Computation of statistical distributions documentation of the program ELV. Second edition can be downloaded at (http://www.stat.uni-muenchen.de/~knuesel/elv/elv_docu.pdf))
10. Knusel L. On the accuracy of statistical distributions in Microsoft Excel 2003. Comput. Statist. Data Anal. 48 3 (2005) 445-449
11. McCullough B.D. Assessing the reliability of statistical software: Part I. Amer. Statist. 52 4 (1998) 358-366
12. McCullough B.D. Assessing the reliability of statistical software: Part II. Amer. Statist. 53 2 (1999) 149-159
13. McCullough B.D., and Vinod H.D. The numerical reliability of econometric software. J. Econom. Literature 37 2 (1998) 633-655
14. McCullough B.D. The accuracy of mathematica 4 as a statistical package. Comput. Statist. 15 (2000) 279-299
15. Pierre, L'Ecuyer, 2007. Stochastic Simulation in Java. Java Documentation Available at (http://www.iro.umontreal.ca/~simardr/ssj/doc/html/overview-summary.html )
16. R Development Core Team, 2008. R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0, Available at (http://www.R-project.org)
17. SourceForge.net, 2007. JSci- A Science API for Java, Java Documentation Available at (http://jsci.sourceforge.net/api/index.html)
18. The Apache Software Foundation, 2007. Jakarta Commons Math API. Java Documentation Available at (http://commons.apache.org/math/api-1.1/index.html)
19. University of California, Los Angeles, 2007. SOCR (Statistics Online Computational Resource). Java Documentation Available at (http://socr.ucla.edu/docs/index.html)
20. Visual Numerics, 2007. JMSL Numerical Library User's Guide Volume 1, 2 and 3 can be downloaded at (http://www.vni.com/books/dod/pdf/jmsl/reference30.pdf)
21. ® Excel 2007. Comput. Statist. Data Anal. (in press), Corrected Proof, Available online 12 March 2008. Advance online publication. Retrieved January 22, 2007. doi:10.1007/s00213-006-0597-7