[BioC] Tools for Combining Affy and aCGH data

[Benjamin Otto]

Hi Torun,

Like Sean I too don't know of any currently available package to do so.
However have a look at the following papers:

1. Stranger et. al.:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=17
289997

2. Spielman et. al.:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=17
206142

3. Chin et. al:
http://linkinghub.elsevier.com/retrieve/pii/S1535610806003151


Benjamin


======================================
Benjamin Otto
University Hospital Hamburg-Eppendorf
Institute For Clinical Chemistry
Martinistr. 52
D-20246 Hamburg

Tel.: +49 40 42803 1908
Fax.: +49 40 42803 4971
======================================


-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Sean Davis
Gesendet: Saturday, July 07, 2007 9:25 PM
An: Tarun Nayar
Cc: bioconductor at stat.math.ethz.ch
Betreff: Re: [BioC] Tools for Combining Affy and aCGH data

Tarun Nayar wrote:
> Hi,
>  
> Are there any tools out there to combine/ compare Affy gene expression 
> and aCGH data? A collaborator has 12 aCGH expts and 12 affy expression 
> chips from the same biological samples. He's interested in seeing if 
> regions of CN alteration correspond to differences in gene expression.
> We've taken a stab at writing our own program for this, now I'm 
> wondering if there are any pre-made tools to do the same.
>   

I don't know of R/bioc packages for doing this directly, but some version of
correlation between CGH measurements and gene expression measures is
probably useful.  You can use standard R commands to do this.  Within any
region of amplification, note that there will likely be only a portion (of
unknown quantity) of gene expression that is correlated with copy number.

Sean

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