Optimization of a Parallel permutation testing function for the SPRINT R package

HPDC 2010 - Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing

Volumn , Issue , 2010, Pages 516-521

  Petrou, Savvas ^a   Sloan, Terence M ^a   Mewissen, Muriel ^b   Forster, Thorsten ^b   Piotrowski, Michal ^a   Dobrzelecki, Bartosz ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

HPC; Microarray; MPI; Permutation

Indexed keywords

COMPUTING INFRASTRUCTURES; HIGH PERFORMANCE COMPUTING SYSTEMS; HPC; MICROARRAY DATA; MPI; PERMUTATION; PERMUTATION TESTING;

BIOINFORMATICS; SUPERCOMPUTERS;

DATA HANDLING;

EID: 78650013528     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1851476.1851551     Document Type: Conference Paper

References (13)

1. The R package, "The R Project for Statistical Computing." Available at : http://www.r-project.org/, accessed 20 February 2010.
2. Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M Sloan, Florian Scharinger, Arthur Trew and Peter Ghazal, "SPRINT: A new parallel framework for R," BMC Bioinformatics, December 2008.
3. SPRINT's website, "SPRINT: A new parallel framework for R." Available at : http://www.r-sprint.org/, accessed 20 February 2010.
4. M. Mewissen, "SPRINT-User Requirements Survey Results." Technical report from Wellcome Trust, Grant WT086696MA, July 24th 2009.
5. Y. Ge, S. Dudoit and T. P. Speed, "Resampling-based multiple testing for microarray data hypothesis," vol. 12, pp. 1-77, June 2003.
6. The multtest R package, "multtest: Resampling-based multiple hypothesis testing." Available at : http://cran.rproject.org/web/packages/ multtest/index.html,accessed 20 February 2010.
7. NWS, "NetWorkSpaces for R." Available at : http://nws-r. sourceforge.net/, accessed 3 March 2010.
8. Rmpi, "Rmpi for R." Available at : http://www.stats.uwo.ca/ faculty/yu/Rmpi/, accessed 3 March 2010.
9. R/parallel, "R/parallel framework." Available at : http://www.rparallel.org/, accessed 3 March 2010.
10. papply, "papply-R parallel apply function." Available at : http://math.acadiau.ca/ACMMaC/software/papply.html, accessed 3 March 2010.
11. SNOW, "Simple Network of Workstations for R." Available at : http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html, accessed 3 March 2010.
12. Westfall,P.H. and Young, S.S., "Resampling-Based Multiple Testing: Examples and Methods for P-Value Adjustment.," p. 340, 1993. Wiley, New York.
13. HECToR's user support, "HECToR : Hardware overview." Available at : http://www.hector.ac.uk/service/hardware/, accessed 20 February 2010.