Gene coexpression network has been built and kindly provided by Bin. Here I am showing a few graphs I plotted to show the percent variance explained for each module as well as the variability within the first principal component of each module.
Affymetrix, 378 patients, 65 modules:
Agilent, 350 patients, 67 modules:
It seems that Affy has more variability in the values of the first principal component, while Agilent has modules that don't explain much of the variance.