Enrichment Analysis and Pathway Analysis provide different globaltest results


When I use the same metabolites dataset on the Quantitative Enrichment Analysis and Pathway Analysis (human KEGG library used), I am getting different results for the global test. Is this expected?

I have noticed that there are differences in the metabolite sets for KEGG used in QEA and Pathway Analysis. For example, the KEGG library used in QEA does not appear to have “Pyruvate metabolism”. But even for the metabolite set that appear the same on QEA and Pathway Analysis, there are difference in the match status.
For example, for Glycerophospholipid metabolism there are 5/36 match in the QEA but there are 6/36 match in the pathway analysis. 1-Acyl-sn-glycero-3-phosphocholine was not picked up in QEA.

Which global test result should be used for the enrichment analysis (from QEA module or Pathway Analysis module)?

Thank you

Hi Ken,
thanks for reporting your case. I have carefully checked the reason for this different within MetaboAnalyst. That is because the QEA module in Enrichment Analysis is using KEGG compound as the internal identifier, while Pahtway analysis module is using KEGG ID. They are not 100% equal (one compound name may have multiple KEGG IDs). I will gradually update to make them consistently use KEGG ID.
Sorry for this confusion. Hope this help!