Tarun Nayar wrote:
> Are there any tools out there to combine/ compare Affy gene
> and aCGH data? A collaborator has 12 aCGH expts and 12 affy
> chips from the same biological samples. He's interested in seeing if
> regions of CN alteration correspond to differences in gene
> 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.