This is an update of Paired t-test as a special case of linear model and hierarchical model Figure 2A of the paper Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism uses a paired t-test to compare endurance performance in mice treated with a control microbe (Lactobacillus bulgaricus) and a test microbe (Veillonella atypica) in a cross-over design (so each mouse was treated with both bacteria).

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Update – Fig. 2A is an analysis of the maximum endurance over three trials. This has consequences. Figure 2A of the paper Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism uses a paired t-test to compare endurance performance in mice treated with a control microbe (Lactobacillus bulgaricus) and a test microbe (Veillonella atypica) in a cross-over design (so each mouse was treated with both bacteria).

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Update - This post has been updated A very skeletal analysis of Sharon, G., Cruz, N.J., Kang, D.W., Gandal, M.J., Wang, B., Kim, Y.M., Zink, E.M., Casey, C.P., Taylor, B.C., Lane, C.J. and Bramer, L.M., 2019. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. Cell, 177(6), pp.1600-1618. which got some attention on pubpeer. Commenters are questioning the result of Fig1G. It is very hard to infer a p-value from plots like these, where the data are multi-level, regardless of if means and some kind of error bar is presented.

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R doodles. Some ecology. Some physiology. Much fake data.

Thoughts on R, statistical best practices, and teaching applied statistics to Biology majors.

Jeff Walker, Professor of Biological Sciences

University of Southern Maine, Portland, Maine, United States