Hi, Ken, Sean and Philippe,

Thank you for your kind help. The strategy Sean talked about is very
reasonable for me and I guess it can solve the problem. It's great I can try
diferent ways (in R or software) to do it.

Di

On 10/19/06, Lo, Ken <Ken.Lo@roswellpark.org> wrote:
>
> Hi Di,
>
> We have developed some software tools to overlay datasets between aCGH
> (our own RPCI Bac array) and expression (Affymetrix genechips) for
> candidate gene identification that has been submitted for publication.
> If you are interested in trying it out, it should be available in the
> near future.  I could also send you a beta test version, if you'd like.
> Just let me know.  Our solution is pretty much as Sean has described.
> Segmentation followed by giving calls to each segment.  Pairwise
> comparison between normal and disease tissue for genechips.  The overlay
> will be performed by gene symbols (i.e. in the single copy gain in 7p,
> the following genes (by HUGO approved gene symbol) were upregulated...).
> If I understood your problem accurately, we have the tool for it.
>
> Best,
>
> Ken Lo
> Ken.lo@roswellpark.org
>
>
>
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Di Wu
> Sent: Tuesday, October 17, 2006 11:07 PM
> To: Bioconductor@stat.math.ethz.ch
> Subject: [BioC] aCGH and Affymetrix
>
> Dear All,
>
> I have some data contain both aCGH data and affymetrix data. Same
> samples aere used to generate the two types of arrays. aCGH arrays used
> are Agilent custom HD-CGH microaarays(44k). I have the package aCGH in
> R.
>
> I want to combine the two kinds of data together according to chromosome
> location(any other suggestion?), so that I can know the region and gene
> list which both amplified in tumor cell and other catogorical change
> between the two types of data. I can find the way to visualize the
> result along the
> chromosomes: but is there any way to calculate the results by numbers
> and report the region or gene list in a numerical list? I don't want to
> circle all the dot I am interested in by hand, to enlarge them, to see
> what gene are inside.
>
> Anybody with aCGH data analysis experience? please help me out.
>
> Thanks in advance.
> Di
>
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