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ROC curves for Golden Spike data, by known fold chang. With RMA preprocessing, the performance of several methods testing for differential expression is compared using the full 3 × 3 comparison of the Golden Spike spike-in data, treating the eight levels of reported spiked-in fold changes separately. Several methods have difficulty detecting differential expression for spiked-in genes with fold changes 1.5 and 1.7 in particular.
