[BioC] Agilent Human Genome CGH 44K annotation

[Sean Davis]

On Mon, Sep 8, 2008 at 9:37 AM, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:
> Hi,
>
> I am looking for up to date annotation information for Agilent Human
> Genome CGH 44K microarrays (G4426B).  There doesn't seem to be a
> bioconductor package for this array.  Is this correct?  What would be
> the best way to build up to date information for this microarray?

For CGH, the best way (in my opinion) to get up-to-date information is
to align the probes to the reference genome.  You could do this with
blat (from UCSC), gmap, or using the Biostrings package.  This will
give you chromosome locations, obviously.  Once you have done your
segmentation analysis, you can find genes of interest using biomart or
UCSC tables and overlaps.

Sean