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

[J-C. Marioni]

Hi Caimiao,

If you set the argument maxChromThreshold equal to 24, this should prevent 
chromosomes 23 and 24 being excluded from the MA object.

Hope this helps,
John

On Wed, 3 Oct 2007, caiwei at mdanderson.org wrote:

> 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"
>>
>
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