2021
DOI: 10.1371/journal.pone.0259973
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Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods

Abstract: The diet plays a major role in shaping gut microbiome composition and function in both humans and animals, and dietary intervention trials are often used to investigate and understand these effects. A plethora of statistical methods for analysing the differential abundance of microbial taxa exists, and new methods are constantly being developed, but there is a lack of benchmarking studies and clear consensus on the best multivariate statistical practices. This makes it hard for a biologist to decide which meth… Show more

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Cited by 15 publications
(16 citation statements)
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“…Also in Calgaro et al [ 19 ], many of the methods included in our comparison show an average FPR value slightly above the threshold, with the exception of ALDEx2 which holds control correctly. Lastly, Khomich et al [ 20 ] observed a FPR close to 0 for all methods include in their comparison.…”
Section: Discussionmentioning
confidence: 94%
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“…Also in Calgaro et al [ 19 ], many of the methods included in our comparison show an average FPR value slightly above the threshold, with the exception of ALDEx2 which holds control correctly. Lastly, Khomich et al [ 20 ] observed a FPR close to 0 for all methods include in their comparison.…”
Section: Discussionmentioning
confidence: 94%
“…Furthermore, Lin et al [ 13 ] find that ALDEx2 has smaller recall values as compared to competing DA methods, but in general the values ​​are higher than observed in the previous benchmark study for similar sample size values. Finally, Khomich et al [ 20 ] conclude that DESeq2 and ALDEx2 perform poorly in term of recall values, as opposed to ANCOM when the percentage of DA taxa is low.…”
Section: Discussionmentioning
confidence: 99%
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“…The variation in microbiota at phylum and genus level were decomposed by analysis of variance simultaneous component analysis (ASCA) ( 40 , 41 ). The ASCA model contained a Subject effect, accounting for the between subject variation, and an intervention-specific visit effect.…”
Section: Methodsmentioning
confidence: 99%