Table 2 Significant pathways with at least 5 matched significant metabolic features for parameter settings where ~ 4,000 features were detected.
From: Addressing the batch effect issue for LC/MS metabolomics data in data preprocessing
Pathways | Overlap_size | Pathway_size | p value |
|---|---|---|---|
Two-stage apLCMS (within-batch proportion 0.3, initially detected in at least 4 batches), 4,034 features | |||
Lysine metabolism | 6 | 19 | 0.00185 |
Phosphatidylinositol phosphate metabolism | 5 | 16 | 0.00479 |
Butanoate metabolism | 5 | 17 | 0.00681 |
Glycine, serine, alanine and threonine metabolism | 8 | 38 | 0.00798 |
Aspartate and asparagine metabolism | 9 | 52 | 0.01899 |
Urea cycle/amino group metabolism | 7 | 40 | 0.02756 |
Pyrimidine metabolism | 5 | 27 | 0.0463 |
Glycerophospholipid metabolism | 8 | 53 | 0.04966 |
Traditional apLCMS (minimum samples detected 90), 4,129 features | |||
Butanoate metabolism | 5 | 15 | 0.00387 |
Glycine, serine, alanine and threonine metabolism | 8 | 37 | 0.00689 |
Arachidonic acid metabolism | 6 | 24 | 0.00748 |
Lysine metabolism | 5 | 18 | 0.0079 |
Vitamin B3 (nicotinate and nicotinamide) metabolism | 5 | 18 | 0.0079 |
Glycerophospholipid metabolism | 9 | 52 | 0.01681 |
Urea cycle/amino group metabolism | 7 | 43 | 0.041 |
Aspartate and asparagine metabolism | 8 | 53 | 0.04899 |
XCMS (centWave + loess, IPO optimized, minimum samples detected 90), 4,165 features | |||
C21-steroid hormone biosynthesis and metabolism | 6 | 24 | 0.00395 |
Urea cycle/amino group metabolism | 5 | 30 | 0.04353 |
