running time of snapCGH processCGH and runDNAcopy
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@caiweimdandersonorg-1599
Last seen 7.1 years ago
Dear list, I am running snapCGH (1.4.0) in R 2.5.1 on a sun-solaris2.9 with 25 Agilent mouse 244K CGH arrays. I run the processCGH function for 2 days, and before I get this job done, the program just froze and quit without giving me any result. If I only run two arrays at a time, it takes about 1.5 hour to run the processCGH function, and about another 1.5 hours to run the runDNAcopy function. Are there any ways to speed up these two steps? Thanks, Caimiao my code lines: MA2<-processCGH(MA1, method.of.averaging=mean, ID='ProbeName',maxChromThreshold = 24) SegInfo.DNAcopy<-runDNAcopy(MA2) > sessionInfo() R version 2.5.1 (2007-06-27) sparc-sun-solaris2.9 locale: C attached base packages: [1] "splines" "grid" "tools" "stats" "graphics" "grDevices" [7] "utils" "datasets" "methods" "base" other attached packages: xtable snapCGH aCGH sma multtest cluster "1.4-6" "1.4.0" "1.10.0" "0.5.15" "1.16.0" "1.11.7" GLAD aws DNAcopy tilingArray pixmap geneplotter "1.10.0" "1.3-3.1" "1.10.0" "1.14.0" "0.4-7" "1.14.0" lattice annotate genefilter survival vsn strucchange "0.15-11" "1.14.1" "1.14.1" "2.32" "2.2.0" "1.3-2" sandwich zoo RColorBrewer affy affyio Biobase "2.0-2" "1.3-2" "1.0-1" "1.14.2" "1.4.1" "1.14.1" limma "2.10.5"
aCGH Survival CGH annotate genefilter affy DNAcopy aCGH GLAD tilingArray snapCGH aCGH • 778 views
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@jhs1jjmleedsacuk-2338
Last seen 7.1 years ago
Hi Caimiao, For me, the DNAcopy segmentation function ran quicker in the actually DNAcopy package than it did in the snapCGH package, not sure why but I do know they made some speed improvements in the CBS algorithm that may not have been implemented in snapCGH. It may be worth investigating using the actual DNAcopy package, especially if snapCGH is crashing on you. If anyone feels this is wrong feel to correct me, just thought I should contribute as I've made heavy use of this mailing list myself! Regards John Quoting caiwei at mdanderson.org on Fri 05 Oct 2007 17:46:58 BST: > > Dear list, > > I am running snapCGH (1.4.0) in R 2.5.1 on a sun-solaris2.9 with 25 > Agilent > mouse 244K CGH arrays. I run the processCGH function for 2 days, > and > before I get this job done, the program just froze and quit without > giving > me any result. If I only run two arrays at a time, it takes about > 1.5 > hour to run the processCGH function, and about another 1.5 hours to > run the > runDNAcopy function. > > Are there any ways to speed up these two steps? > > Thanks, > > Caimiao > > > my code lines: > MA2<-processCGH(MA1, method.of.averaging=mean, > ID='ProbeName',maxChromThreshold = 24) > SegInfo.DNAcopy<-runDNAcopy(MA2) > > > sessionInfo() > R version 2.5.1 (2007-06-27) > sparc-sun-solaris2.9 > > locale: > C > > attached base packages: > [1] "splines" "grid" "tools" "stats" "graphics" > "grDevices" > [7] "utils" "datasets" "methods" "base" > > other attached packages: > xtable snapCGH aCGH sma multtest > cluster > "1.4-6" "1.4.0" "1.10.0" "0.5.15" "1.16.0" > "1.11.7" > GLAD aws DNAcopy tilingArray pixmap > geneplotter > "1.10.0" "1.3-3.1" "1.10.0" "1.14.0" "0.4-7" > "1.14.0" > lattice annotate genefilter survival vsn > strucchange > "0.15-11" "1.14.1" "1.14.1" "2.32" "2.2.0" > "1.3-2" > sandwich zoo RColorBrewer affy affyio > Biobase > "2.0-2" "1.3-2" "1.0-1" "1.14.2" "1.4.1" > "1.14.1" > limma > "2.10.5" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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jhs1jjm at leeds.ac.uk wrote: > Hi Caimiao, > > For me, the DNAcopy segmentation function ran quicker in the actually > DNAcopy package than it did in the snapCGH package, not sure why but I > do know they made some speed improvements in the CBS algorithm that may > not have been implemented in snapCGH. It may be worth investigating > using the actual DNAcopy package, especially if snapCGH is crashing on > you. If anyone feels this is wrong feel to correct me, just thought I > should contribute as I've made heavy use of this mailing list myself! Hi, John. Just to clarify, snapCGH uses the DNAcopy package. They are not different implementations. Sean
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On 10/5/07, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > jhs1jjm at leeds.ac.uk wrote: > > Hi Caimiao, > > > > For me, the DNAcopy segmentation function ran quicker in the actually > > DNAcopy package than it did in the snapCGH package, not sure why but I > > do know they made some speed improvements in the CBS algorithm that may > > not have been implemented in snapCGH. It may be worth investigating > > using the actual DNAcopy package, especially if snapCGH is crashing on > > you. If anyone feels this is wrong feel to correct me, just thought I > > should contribute as I've made heavy use of this mailing list myself! > > Hi, John. > > Just to clarify, snapCGH uses the DNAcopy package. They are not > different implementations. I haven't looked at the snapCGH code, but in case it is truly slowing things down, keep an eye on the memory overhead of your R process. If you're running low of memory and your OS start swapping you'll experience a 10-1000x slowdown. It might be that snapCGH is creating extra/unnecessary copies. My $.02 /Henrik > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Henrik Bengtsson wrote: > On 10/5/07, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> jhs1jjm at leeds.ac.uk wrote: >>> Hi Caimiao, >>> >>> For me, the DNAcopy segmentation function ran quicker in the actually >>> DNAcopy package than it did in the snapCGH package, not sure why but I >>> do know they made some speed improvements in the CBS algorithm that may >>> not have been implemented in snapCGH. It may be worth investigating >>> using the actual DNAcopy package, especially if snapCGH is crashing on >>> you. If anyone feels this is wrong feel to correct me, just thought I >>> should contribute as I've made heavy use of this mailing list myself! >> Hi, John. >> >> Just to clarify, snapCGH uses the DNAcopy package. They are not >> different implementations. Looking at the runDNAcopy code, it does the smooth.CNA step as well as running DNAcopy::segment(); that probably explains the slowdown when using runDNAcopy. Sean
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