Ranking of gene set analysis methods under several scenarios.

Datasets were divided into small sample size and large sample size using the median of sample sizes, 22, as cut-off. Similarly, the datasets were divided according to the number of genes in the target gene set using the median of gene set sizes, 66, as cut-off. Of the 42 experiments 11 were paired and 31 were not paired designs. To quantify the effect size, datasets were divided into a small effect group and a large effect group based on the % of genes with p<0.05, with the cut-of point being 24.6%.