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. 2020 Mar 9;22(1):545–556. doi: 10.1093/bib/bbz158

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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Random sample labels and random gene sets. (a) Type I error rates (-axis) as evaluated on the dataset from Golub et al. [42] by shuffling sample labels 1000 times and assessing in each permutation the fraction of gene sets with . Gene sets were defined according to GO-BP (). Blue points indicate the mean type I error rate and the red dashed line the significance level of 0.05. The gray dashed line divides methods based on the type of null hypothesis tested [6]. *Application of CAMERA without accounting for inter-gene correlation (default: inter-gene correlation of 0.01). Supplementary Figure S5 shows type I error rates when using KEGG gene sets. Supplementary Figure S6 shows type I error rates for all four combinations of benchmark compendium and gene set collection. (b) Percentage of significant gene sets (, -axis) when applying methods to the Golub dataset (true sample labels) and using 100 randomly sampled gene sets of defined size (-axis). Shown is the mean standard deviation (gray bands) across 100 replications of the simulation experiment.

Inline graphic — Random sample labels and random gene sets. (a) Type I error rates (-axis) as evaluated on the dataset from Golub et al. [42] by shuffling sample labels 1000 times and assessing in each permutation the fraction of gene sets with . Gene sets were defined according to GO-BP (). Blue points indicate the mean type I error rate and the red dashed line the significance level of 0.05. The gray dashed line divides methods based on the type of null hypothesis tested [6]. *Application of CAMERA without accounting for inter-gene correlation (default: inter-gene correlation of 0.01). Supplementary Figure S5 shows type I error rates when using KEGG gene sets. Supplementary Figure S6 shows type I error rates for all four combinations of benchmark compendium and gene set collection. (b) Percentage of significant gene sets (, -axis) when applying methods to the Golub dataset (true sample labels) and using 100 randomly sampled gene sets of defined size (-axis). Shown is the mean standard deviation (gray bands) across 100 replications of the simulation experiment.