[BioC] problem with analyzing human 244k agilent array with snapCGH

[Sean Davis]

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