[BioC] analyzing genomic hybridization data with limma?

[Sean Davis]

On Friday 01 December 2006 12:04, Erik Dopman wrote:
> Hi all,
>
> I was wondering if anybody knows whether it is appropriate to analyze
> genomic hybridizations using limma? I assume no because the data are so
> different from mRNA hybs, but I am not sure. Any thoughts or comments
> are appreciated.

Limma is a very good tool, but for CGH data, there are more applicable tools.  
snapCGH combines many of them and allows one to use limma tools for loading 
data and normalization.  Note that the approach to normalization for CGH is 
also somewhat different than for typical expression arrays.  

Sean