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

[Sean Davis]

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!

The help for processCGH will answer that question.  In short, the
maxChromThreshold argument has a default of 22.

Sean