Normalization

Affymetrix
MAS 5.0 expression values were calculated based on scaling to a target intensity of 100, then transformed by Log2(x+20).
Calls were computed using the MAS5.0 present/absent algorithm.
Codelink
Expression values were median scaled to a target intensity of 66 (the overall median), then transformed by Log2(x+20).
Genes with a G call were called present, other calls were called absent.
cDNA
Cy5 foreground and Cy5 background were computed using loess normalization. Next, Cy5 foreground Cy5 background was calculated. These values were median scaled to a target intensity of 985 (the overall median), then log base 2 transformed.
Genes were called present if they had no quality flags, and if their Cy5/Cy3 ratio was above the 96% quantile of ratios for control genes.
Agilent
Cy5 (or Cy3 for dye-swaps) expression values were calculated based on loess normalized signals. These values were median scaled to a target intensity of 640 (the overall median) then averaged across dye-swap replicates.
Genes were called present if their Cy5 (or Cy3 for dye-swaps) value was above the 96% quantile for control genes.
Cross Study Normalization
Expression values were further scaled so that the median expression value for each study was equal to 100 on the linear (non-logged) scale.