Reply to: Examining microbe–metabolite correlations by linear methods

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dc.contributor.authorMorton, James T.
dc.contributor.authorMcDonald, Daniel
dc.contributor.authorAksenov, Alexander A.
dc.contributor.authorNothias, Louis Felix
dc.contributor.authorFoulds, James R.
dc.contributor.authorQuinn, Robert A.
dc.contributor.authorBadri, Michelle H.
dc.contributor.authorSwenson, Tami L.
dc.contributor.authorGoethem, Marc W. Van
dc.contributor.authorNorthen, Trent R.
dc.contributor.authorVazquez-Baeza, Yoshiki
dc.contributor.authorWang, Mingxun
dc.contributor.authorBokulich, Nicholas A.
dc.contributor.authorWatters, Aaron
dc.contributor.authorSong, Se Jin
dc.contributor.authorBonneau, Richard
dc.contributor.authorDorrestein, Pieter C.
dc.contributor.authorKnight, Rob
dc.date.accessioned2021-02-05T17:55:22Z
dc.date.available2021-02-05T17:55:22Z
dc.description.abstractQuinn and Erb propose to apply a centered log-ratio (CLR) transform before performing correlation analysis and make the case that, when used correctly, correlation and proportionality can outperform MMvec in identifying microbe–metabolite interactions. While this may be an appealing strategy, it is important to note that the correlations estimated from CLR-transformed data will have a fundamentally different interpretation than the true correlations in the environment, namely: Cov xi; yj ≠Cov clr(x)i, clr(y)j where xi and yj are the absolute abundances for microbe abundances x and metabolite abundances y in taxon i and metabolite j. Because the absolute abundances are often not available, inferring the true correlations between microbes and metabolites is not tractable (Supplementary Note 1). This phenomenon has been extensively studied in refs. 2–4 , and one of our recent studies provides the intuition behind this in the case of differential abundance . Because of this discrepancy, we proposed to use co-occurrence probabilities instead of correlation.en_US
dc.description.urihttps://www.nature.com/articles/s41592-020-01007-0en_US
dc.format.extent5 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2fjrn-xakm
dc.identifier.citationMorton, J.T., McDonald, D., Aksenov, A.A. et al. Reply to: Examining microbe–metabolite correlations by linear methods. Nat Methods 18, 40–41 (2021). https://doi.org/10.1038/s41592-020-01007-0en_US
dc.identifier.urihttps://doi.org/10.1038/s41592-020-01007-0
dc.identifier.urihttp://hdl.handle.net/11603/20954
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Information Systems Department Collection
dc.relation.ispartofUMBC Faculty Collection
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dc.rightsPublic Domain Mark 1.0*
dc.rightsThis work was written as part of one of the author's official duties as an Employee of the United States Government and is therefore a work of the United States Government. In accordance with 17 U.S.C. 105, no copyright protection is available for such works under U.S. Law.
dc.rights.urihttp://creativecommons.org/publicdomain/mark/1.0/*
dc.titleReply to: Examining microbe–metabolite correlations by linear methodsen_US
dc.typeTexten_US

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