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关于"同样的代码和数据，GSEA 两次运行结果不一样"

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TL;DR - clusterProfiler developers explain why identical GSEA inputs can produce different results and report fixes restoring explicit seed control and historical filtering behavior. Reproducibility requires a fixed seed and recorded package versions and methods.

  • Unseeded multilevel Monte Carlo sampling can move borderline pathways across significance thresholds.
  • clusterProfiler 4.19.3+ switched from simple permutation to the fgsea-recommended multilevel method, causing legitimate version-dependent differences.
  • enrichit 0.2.1 and clusterProfiler 4.21.1 restore explicit seed support and dual pvalue/p.adjust filtering.
  • Expanding gene-set sizes and setting pvalueCutoff = 1 does not ensure reproducibility; seed = 123 or set.seed(123) does.

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关于"同样的代码和数据，GSEA 两次运行结果不一样"

WeChat: 生信技能树 2026-08-15
Public signals N/A
Providers: Hugging Face · N/A OpenAlex · N/A Publisher · N/A Semantic Scholar · N/A X · N/A Fetched 2026-09-17 14:33:01.907906 UTC

TL;DR - clusterProfiler developers explain why identical GSEA inputs can produce different results and report fixes restoring explicit seed control and historical filtering behavior. Reproducibility requires a fixed seed and recorded package versions and methods.

  • Unseeded multilevel Monte Carlo sampling can move borderline pathways across significance thresholds.
  • clusterProfiler 4.19.3+ switched from simple permutation to the fgsea-recommended multilevel method, causing legitimate version-dependent differences.
  • enrichit 0.2.1 and clusterProfiler 4.21.1 restore explicit seed support and dual pvalue/p.adjust filtering.
  • Expanding gene-set sizes and setting pvalueCutoff = 1 does not ensure reproducibility; seed = 123 or set.seed(123) does.
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