On Wed, Mar 26, 2008 at 11:45 AM, Sergii Ivakhno
<sergii.ivakhno at="" cancer.org.uk=""> wrote:
> Hello,
> I'm using the snapCGH package to analyse human 244k agilent CGH
arrays.
> targets <- readTargets ("targets.txt")
> RG1 <-read.maimages (targets$File_names, source="agilent")
> RG2 <- readPositionalInfo (RG1,source="agilent")
>
> Unfortunately, when I want to extract chromosome information is
appears
> that chromosomes 20,21 and 22
> are missing from the RG2 obgect
> table(RG2$genes$Chr)
> 2 3 4 5 6 7 8 9 10 11 12 13
> 16394 16856 13133 13642 13993 14135 13618 11524 12045 11833 12658
10343
> 10644
> 14 15 16 17 18 19 23 24
> 10687 9327 9041 9013 8058 6391 12085 599
>
> The same results are obtained when directly accessing RG1 object.
Hi, Sergii.
It looks like you are missing chromosome 1, also? I quickly added the
numbers you have given here and come up with 236,000+ probes. That is
pretty close to the maximum number of usable probes on a 244k array.
Have you looked at the .txt files to see if chr20, chr21, chr22, or
chr1 are represented on your array?
Sean
