[BioC] aCGH package - performance Issues

Diaz.Ramon rdiaz at cnio.es
Tue May 6 11:19:36 CEST 2008

Dear Julian,

We have parallelized (over arrays or arrays * chromosomes) the calls to find.hmm (as well as other aCGH methods) using MPI. The R code is available from the ADaCGH package from CRAN. (The paper describing the approach, showing benchmarks, etc, is available from http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000737). 



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Julian Lee
Sent: Tue 06-May-08 11:03
To: bioconductor
Subject: [BioC] aCGH package - performance Issues
Hi all,

I would like to know if there's a way to tweak the performance of the aCGH package, particularly the find.hmm.states function

Input dataset
Agilent CNV
31 samples
200,000 clones

2 Intel Xeon Dual Core 3GHz (total of 4CPUs)
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:
[1] tools     splines   stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] aCGH_1.14.0     sma_0.5.15      multtest_1.20.0 Biobase_2.0.0  
[5] survival_2.34-1 cluster_1.11.10

Function Call

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.


thank you

Julian Lee
Bioinformatics Specialist
Cellular and Molecular Research
National Cancer Center Singapore

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