The ranking of algorithms was generally consistent regardless of which algorithm was chosen to determine calls in the verification set. DESeq2 had comparable sensitivity to edgeR and voom though less than DSS. The median sensitivity estimates were typically between 0.2 and 0.4 for all algorithms. That all algorithms had relatively low median sensitivity can be explained by the small sample size of the evaluation set and the fact that increasing the sample size in the verification set increases power. It was expected that the permutation-based SAMseq method would rarely produce adjusted P value <0.1 in the evaluation set, because the three vs three comparison does not enable enough permutations.
