Revisiting microbe-metabolite interactions: doing better than random
James T. Morton,
Alexander A. Aksenov,
Louis Felix Nothias,
James R. Foulds,
Robert A Quinn,
Michelle H. Badri,
Tami L Swenson,
Marc W. Van Goethem,
Nicholas A. Bokulich,
Se Jin Song,
Pieter C. Dorrestein,
Posted 16 Dec 2019
bioRxiv DOI: 10.1101/2019.12.10.871905
Posted 16 Dec 2019
Recently, Quinn and Erb et al made the case that when used correctly, correlation and proportionality can outperform MMvec when identifying microbe-metabolite interactions. We revisit this comparison and show that the proposed correlation and proportionality are outperformed by MMvec on real data due to their inability to deal with sparsity commonly observed in microbiome and metabolome datasets.
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