DA.aov/DA.lao and DA.TukeyHSD about datest

[Russel88]

Can you try running a Tukey test just on one of the OTUs:
TukeyHSD(results[[1]])
Is there any output from this?

Also, what version of R and DAtest are you using?

[DitteOL]

I'm using version 2.7.11

t<-TukeyHSD(results[[1]])

Output:
Tukey multiple comparisons of means
95% family-wise confidence level

Fit: aov(formula = as.formula(form))

$predictor
diff lwr upr p adj
GF-BB -2.033594e-07 -0.0001514614 0.0001510547 0.9978192

[Russel88]

Ahh. With only two classes in the predictor (GF and BB) there is no need to run the TukeyHSD, it's designed for >2 classes.

testDA shouldn't run lao, aov and llm2 when you only have two classes in the predictor. Did you use another phyloseq object for this? If you did use the same object, try re-running testDA with the predictor converted to a character:
sample_data(BB_GF)$Mouse_classification2 <- as.character(sample_data(BB_GF)$Mouse_classification)
res <- testDA(BB_GF, "Mouse_classification2")

[DitteOL]

Ahh I'm sorry for my ignorance! It seem to be working now. Thank you for taking the time and answering me so quickly. I hope that if I encounter other problems I can contact you again.
And I will of cause remember to cite the functions I'am ending up using from your package 👍