[BioC] running time of snapCGH processCGH and runDNAcopy

[caiwei at mdanderson.org]

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"