Methods used at each stage of analysis to identify DEGs. "None" indicates that a given step was not performed. Several combined or stand-alone methods were also evaluated, including multi-mgmos, PerfectMatch, GoldenSpike, Alchemy and default settings of GCRMA, RMA, and MAS 5.0 (see Methods). Methods that clearly outperformed other methods in the Platinum Spike dataset are circled in red. The same methods were also applied to the Golden Spike dataset, where the technical and conditional normalization groups are identical. Methods that clearly outperform other methods in the corresponding steps are circled in blue.