[BioC] Chromosome 23 and 24 dropped after run snapCGH processCGH

[caiwei at mdanderson.org]

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"
>