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The metric that you selected in the Metric for ranking genes parameter (Signal2Noise or tTest) requires that you have at least three samples for each phenotype. You have too few samples for at least one of the phenotypes selected in the Phenotype labels parameter .

To analyze a categorical phenotype that has fewer than three samples, use one of the following ranking metrics:

  • Ratio_of_classes
  • log2_Ratio_of_classes
  • Diff_of_classes


For information about the metrics, see the Metric for ranking genes parameter on the Run GSEA Page in the GSEA User Guide.
For information about phenotypes, see Phenotype Labels in the GSEA User Guide.

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