[BioC] Tools for Combining Affy and aCGH data

[Sean Davis]

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