Probe values were normalized to negative control probes by dividing the value of the probe by the maximum negative control probe. Probe values were floored to a normalized value of 3 (3-fold higher than maximum negative control). Probes with no value greater than this floor across all samples were removed from the analysis. The values were log transformed. To control for variability between runs and different input material amounts, we normalized all samples simultaneously using the quantile normalization approach described above. The result is a set of normalized log-expression values for each probe normalized across all experiments.
