I am using MetaboAnalyst to compare two LC-MS treatment groups. After an unpaired t-test I uploaded the significant metabolites and obtained several pathways with low p-values, indicating they are perturbed between the groups.
Could you please advise on the best way to decide whether a significant pathway is overall up-regulated or down-regulated? Specifically:
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Does the Pathway Analysis output include a built-in aggregate metric that already captures pathway directionality?
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If not, is the recommended approach to interpret per-metabolite fold-changes and calculate an aggregate statistic externally?
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Is there a workflow you suggest when describing pathway directionality in a manuscript?