Enrichment Methods:
- Fisher's Exact Test: Classic hypergeometric test with p-value cutoff (original MetaboAnalystR approach)
- GSEA-style: Ranks ALL features without arbitrary cutoff - more stable to threshold changes
- Weighted Enrichment: Uses continuous p-values/t-scores as weights - no binary cutoff
Key Improvements:
- HMDB database instead of KEGG (larger, more comprehensive)
- Multiple statistical approaches for robustness
- Multiple testing corrections (FDR, Bonferroni, Holm)
- Method comparison to assess result stability
Input Data Format
Your file should be tab-delimited with these columns:
- m.z: Mass-to-charge ratio (required)
- p.value: Statistical p-value from your differential analysis (required)
- t.score: T-statistic or fold-change (required)
- mode: positive/negative (required if using mixed mode)