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

[Sean Davis]

On Fri, Mar 28, 2008 at 9:41 AM, Sergii Ivakhno
<Sergii.Ivakhno at cancer.org.uk> wrote:
> Hi Sean,
>  Thanks for your advice (!) and sorry for the direct enquiry.  Neither of
>  the chromosomes are
>  represented on the array. Do you know where the problem can be as I am
>  not involved in
>  the actual data generation  - should I look for updated version of
>  Agilent annotation for bioconductor?

Sergii,

You will need to get in touch with the people who generated the data.
>From them, you will need to get the specific information about the
array design.  If in doubt, you or they can contact Agilent with the
barcodes from the arrays and try to get details from Agilent, but I
would definitely start locally with your laboratory collaborators.
The problem you are having does not seem to be related to bioconductor
and there is no bioconductor annotation involved when using snapCGH.
In fact, it sounds like bioconductor is working just fine.  You will
need to track down the problem from the laboratory/data generation
end.

Hope that helps,
Sean


>  -----Original Message-----
>  From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean
>  Davis
>  Sent: 26 March 2008 16:06
>  To: Sergii Ivakhno
>  Cc: bioconductor at stat.math.ethz.ch
>  Subject: Re: [BioC] problem with analyzing human 244k agilent array with
>  snapCGH
>
>  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
>