[BioC] aCGH package - performance Issues
julian at omniarray.com
Tue May 6 11:03:33 CEST 2008
I would like to know if there's a way to tweak the performance of the aCGH package, particularly the find.hmm.states function
2 Intel Xeon Dual Core 3GHz (total of 4CPUs)
4 GB RAM
Windows 2003 Server Edition
R version 2.7.0 (2008-04-22)
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
 tools splines stats graphics grDevices utils datasets
 methods base
other attached packages:
 aCGH_1.14.0 sma_0.5.15 multtest_1.20.0 Biobase_2.0.0
 survival_2.34-1 cluster_1.11.10
I am familiar with OpenMP. Is it possible to include these openMP pragmas into the function to speed up the computation? This is a concern as i will be moving onto an Illumina SNP dataset with 59 samples and 400,000 clones.
Or would running it on a Linux machine be faster?
dear moderators, Please direct me to the right forum if you think that this should be on the BioC-Dev mailing list instead.
Cellular and Molecular Research
National Cancer Center Singapore
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