Figure 4

RPS variance results for the wholly defined control dataset. The log average RPS variances for expression summary datasets generated from combinations of options from different probe set algorithms. RPS variances were computed at 8 levels with fold change equal to or greater than 1.0, 1.2, 1.5, 1.7, 2.0, 2.5, 3.0, 3.5, or 4.0 between two test sample groups. (a) All 110 expression summary datasets for the comparison of normalization options at the probe set level (b-f). To match the analysis from Choe et al. [14], only 55 expression summary datasets involving the second normalization step are shown. (b) Comparison of expression summary options. (c) Comparison of normalization options. (d) Comparison of PM correction options. (e) Comparison of background correction options. (f) Comparison of the selected 10 expression summary datasets to all others.