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caiwei@mdanderson.org
▴
110
@caiweimdandersonorg-1599
Last seen 10.2 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"