Adonis2 output look different than examples - what do I do wrong?

[KatrineGraversen]

Hi community,

I am not very strong in R and it is the first time I post a questions.
I am using R version 4.4.3 and vegan version 2.6-10.

I am analysing RNAseq data from lab mice. My df consists of 23 mice x 22379 genes + a lot of metadata (treatment, time, sex, litter, cage)

I want to do this
dist<-vegdist(gene_counts_transposed_plotting[,c(13:22391)], method='bray')
adonis2(dist ~ Treatment*Time, data = sampleData, permutations = 999, method = 'bray')

Output:
Permutation test for adonis under reduced model
Permutation: free
Number of permutations: 999

adonis2(formula = dist ~ Treatment * Time, data = sampleData, permutations = 999, method = "bray")
Df SumOfSqs R2 F Pr(>F)
Model 3 0.21195 0.27866 2.4466 0.039 *
Residual 19 0.54866 0.72134
Total 22 0.76061 1.00000

Signif. codes: 0 ‘’ 0.001 ‘’ 0.01 ‘’ 0.05 ‘.’ 0.1 ‘ ’ 1

I don't understand why it just gives me the significance of Model and not the significance of the individual factors as it does in all examples I have found on the internet.

I can also show my problem without my own data:

Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(12)/2
Schizachyrium <- with(dat, as.numeric(field) - as.numeric(NO3)+2) +rnorm(12)/2
Y <- data.frame(Agropyron, Schizachyrium)
dist<-vegdist(Y, method='bray')
adonis2(dist ~ NO3, data = dat, permutations = 999)

Output:
Permutation test for adonis under reduced model
Permutation: free
Number of permutations: 999

adonis2(formula = dist ~ NO3, data = dat, permutations = 999)
Df SumOfSqs R2 F Pr(>F)
Model 1 0.026465 0.10869 1.2195 0.28
Residual 10 0.217018 0.89131
Total 11 0.243483 1.00000

The example comes from this thread: #427
Where the output always says NO3 and not Model...

Can anyone tell me what I should do differently to get estimates for each factor and not Model?
Thanks a lot in advance!
Katrine

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[gavinsimpson]

Please read, either the help for the function you are using, or the other discussions here that cover exactly your question.

Read ?adonis2 and in particular the by argument for ways to get the output you want, but do read what the other types actually do as they may not really be what you want.

[gavinsimpson]

For more, see #694