I would also like to carry out a pathway analysis in MetaboAnalyst 6.0 and have a specific question for which I would like your help. In my analysis, I obtained the following amino acids: Aminobutyric acid, L-Arginine, Glutamine, L-Cysteine, ,Histidine, Lysine, Methyl-Histidine, Taurine, Pipecolic acid, Citrulline. If I enter these without a reference data set, I get two significantly altered pathways in MetaboAnalyst 6.0: arginine biosynthesis and taurine and hypotaurine metabolism. If I enter all other measured amino acids as a reference, there are no more significant changes in the pathway analysis. How can this be explained? Here are two pictures with the results.
It is hard to pinpoint the issue as you did not follow our post guideline.
Basically, providing more compounds (as input list) does not guarantee that there will be more significant pathways or matches. Those compounds must belong to a pathway AND are significantly changed.
When you provide more compounds as reference metabolome, but it is very small - there is no much power either. The enrichment test is more effective for decent sized groups (or sets) containing at least 5 members. In your case, there is only one or two members left per pathway - the pathway coverage is too small to draw confident conclusion.
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