I've been using cDNA spotted arrays for a little while, and now we're
at a point where we'd like to make use of certain arrays provided by
Nimblegen, which are essentially Affymetrix style (only created with a
slightly different technology) and I'm trying to familiarise myself
with the different way to normalise and analyse data in this system...
This prompted the question to me... actually two questions:
1) what would make someone choose one or another method?
2) why doesn't anyone use two colour hybs on Affymetrix style arrays?
1-colour systems seem efficient when one wants to compare a reference
or two with many different samples. Also one avoids the dye-bias
issue... Is there anything else important that I am missing? why not
use 2-colour hybs also on Affymetrix type chips? are all the Affymetrix
scanners 1-laser only?
I've been doing a little google search but I don't seem to find