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.
