Detection spectra. (a) Partial detection spectra (N = 30, σ = 0.5; complete spectra in Additional data file 1; raw data in Additional data file 5) for the EDF-based methods. (b) Corresponding results for the discrete method with six different thresholds for calling genes differentially expressed (t). The sector radiuses are proportional to the parameter-specific powers. The mappings between sectors and methods are given in the in-figure legends. Key observations: (1) Different ontological analysis methods exhibit distinct detection spectra. (2) The threshold-free methods exhibit higher coverages than the discrete method, that is, they detect more diverse category types. (3) The discrete method, which is currently the most commonly used method, exhibits strong threshold-dependency, that is, it needs tweaking to yield good results. (4) Important differences are seen between the threshold-free methods (commented under Results).