[BioC] General normalization problem that's *similar* to microarrays.

[Alex Bokov]

Hello. I am examining data from a 2D gel experiment, but my question is 
about a broader issue of normalization.

Each gel has been stained with two different dyes, whose respective 
intensities report two different protein features, let's call them A and 
B. The quantity of interest is A/B. The data consists of two 
protein-by-gel matrices of intensities, and I need to normalize them. 
The questions is, which of the following would be the preferrable choice?

1) First do normalize.quantiles() on the A and B matrices individually 
and then calculate A/B.
2) First calculate A/B and then do normalize.quantiles() on that.

Thank you so much!