Comments (4)
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?
from datest.
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))
$predictor
diff lwr upr p adj
GF-BB -2.033594e-07 -0.0001514614 0.0001510547 0.9978192
from datest.
Ahh. With only two classes in the predictor (GF and BB) there is no need to run the TukeyHSD, it's designed for >2 classes.
testDA
shouldn't run lao, aov and llm2 when you only have two classes in the predictor. Did you use another phyloseq object for this? If you did use the same object, try re-running testDA
with the predictor converted to a character:
sample_data(BB_GF)$Mouse_classification2 <- as.character(sample_data(BB_GF)$Mouse_classification)
res <- testDA(BB_GF, "Mouse_classification2")
from datest.
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 👍
from datest.
Related Issues (20)
- min.sample argument in preDA function HOT 1
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from datest.