Hi Kelsey,
I tried doing that and keep getting the same error. What am I missing? Here’s my code:
metadat.sub$Treatmentmod= factor(metadat.sub$Treatment,
levels = c(“Bare”, “Mustard”, “Radish”))
fit_data = Maaslin2(
input_data = otus.r,
input_metadata = metadat.sub,
output = “16S_output.trt”,
fixed_effects = c(“Treatmentmod”),
reference = c(“Bare”,“Mustard”,“Radish”))
It keeps returning this error:
Error in Maaslin2(input_data = otus.r, input_metadata = metadat.sub, output = “16S_output.trt”, :
Please provide the reference for the variable ‘Treatmentmod’ which includes more than 2 levels: Bare, Radish, Mustard.