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I'm not a statistician and kinda working through this blindly, but why does my NMDS plot of bray-curtis measures show clear groupings for status (blue and pink) but adonis says that time point is significantly different?

distance_calc <- phyloseq::distance(rarified2, "bray")
 sampledf <- data.frame(sample_data(rarified2))
 adonisresult<- adonis2(formula = distance_calc ~ Status * Time.Point, data = sampledf, type = "bray")

> adonisresult
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999

adonis2(formula = adonisf, data = sampledf, type = "bray")
                  Df SumOfSqs      R2      F Pr(>F)  
Status             1   0.2534 0.05397 1.2969  0.198  
Time.Point         1   0.4277 0.09111 2.1893  0.016 *
Status:Time.Point  1   0.1061 0.02259 0.5429  0.901  
Residual          20   3.9072 0.83232                
Total             23   4.6943 1.00000                
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

NMDS

DS14
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  • Perhaps because this was the case? Please note that your plot is absolutely invalid: you should have equal aspect ratio meaning that the scaling is the same on x and y axes, but you have stretched the vertical axis (y) two-three-fold. Moreover, NMDS is a a *nonmetric* method whereas adonis is a *metric* method. Anyway, we have no data or other information to reproduce your case. – Jari Oksanen Jan 14 '23 at 22:39
  • @JariOksanen ah thank you i had no idea! – DS14 Jan 14 '23 at 23:28

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