关于"同样的代码和数据，GSEA 两次运行结果不一样"

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.