[BioC] running time of snapCGH processCGH and runDNAcopy

[jhs1jjm at leeds.ac.uk]

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"
>
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