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caiwei@mdanderson.org
▴
110
@caiweimdandersonorg-1599
Last seen 10.2 years ago
Dear list,
I am using snapCGH to look at Agilent's mouse aCGH array. my MAlist
object
(MA1) have chromosomes 1-19, 23 and 24. After I run the processCGH
function, chromosome 23 and 24 are no longer in my new MAlist object
(MA2).
Any idea where the problem is? Thanks!
__________________________
Caimiao Wei, Ph.D.
Senior Statistical Analyst
Division of Quantitative Sciences
UT M.D.Anderson Cancer Center
1515 Holcombe Blvd, Unit 237
Houston, TX 77030-4009
Tel: (713)563-4297
Fax: (713) 792-4262
Office location: HMB13. 200A
> table(MA1$genes$Chr)
1 2 3 4 5 6 7 8 9 10 11
12
13
16283 16856 13062 13658 13977 14156 13570 11538 12058 11879 12658
10443
10693
14 15 16 17 18 19 23 24
10836 9357 9090 9122 8092 6405 12089 612
> MA2<-processCGH(MA1, method.of.averaging=NULL, ID='ProbeName')
> table(MA2$genes$Chr)
1 2 3 4 5 6 7 8 9 10 11
12
13
16283 16856 13062 13658 13977 14156 13570 11538 12058 11879 12658
10443
10693
14 15 16 17 18 19
10836 9357 9090 9122 8092 6405
> 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"
>