[BioC] BioC normalisations for small array 2 colour data?

[Sean Davis]

On Friday 08 September 2006 00:29, you wrote:
bioconductor at stat.math.ethz.ch
> Sean - I agree that normalization methods that are based on assumptions
> of invariance of 'something' between the different colors or arrays can
> (but need not) fail if a large part of genes is differentially expressed
> - but I am not following the argument why 'single-channel' methods would
> be fundamentally different in this respect.

I made an assumption that there might be a common reference which could be 
used (I am not saying exactly HOW it could be used, but if present, should be 
invariant).  

I totally agree that simple single channel normalization is also problematic 
in the situation where all genes are expected to be differentially expressed.  

Sean