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Fig. 3 | BMC Bioinformatics

Fig. 3

From: A strategy for evaluating pathway analysis methods

Fig. 3

Comparison of recall values computed for the six pathway analysis methods, based on the top 20 most significantly up-regulated (a, b) and top 20 most significantly down-regulated pathways (c, d), which each method identified for the Parkinson’s disease dataset. For each box-and-whisker plot, the horizontal line, top and bottom sides of the box, and vertical line show the median, upper and lower quartiles, and range, respectively, of the recall values. The comparisons are separated into two groups for clarity and to distinguish the two different permutation methods. a and c compare methods ORA, GSA, GSEA, and AFC. b and d compare methods GSEAs, GSEA, AFCs, and AFC. The sample size corresponds to the number of samples contained in the sub-datasets randomly resampled from the original datasets

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