The total number of samples used in the model for the association is showing to be 1


I am using Maaslin2 for analysis with only one fixed effect (5 variables, 1 reference). Results are quite interesting but they seem to be invalid as “N” which is the total number of samples used in the model for association is showing out to be 1 per sample.
I also don’t have any data in my significant results table and I believe it is because the total number of samples is showing 1 so they can’t compare.
I will be very grateful if you can help me with this problem.

I am trying to compare path abundances from HUMAnN
Here is my code
fit_data_relab = Maaslin2(input_data = relab_pathabundance_2_2_23, input_metadata = metafile_relab_pathabundance_2_2_23, min_prevalence = 0,normalization = “NONE”,output = “relab_output”,fixed_effects = c(“Case”),reference = c(“Case,T1”))

Thank you again for this very powerful and easy-to-use tool!



I don’t see anything obviously wrong with your command, so it will be hard to diagnose the issue without the data. It might be the variance filter if all but one of your samples are constant. You can review the example data provided in the tutorial to double check that your inputs are formatted correctly.