MaAsLin2 Version ‘1.16.0’

I am analyzing a data set from a longitudinal study including 8 timepoints collected from 9 different individuals. When I run the model specifying only the fixed effect of “Time.Point” the results are as expected. However, when I run the model including the random effects of “SubjectID” the output contains duplicate rows for every feature; in each duplicate row the metadata and value are populated by the names of the variables “Time.Point” and "SubjectID, respectively. The coeff, stderr, pval, and qval are all “NA.” When I use the random effect as the fixed effect, it works as expected.

Code:

#this works

maaslin_res ← Maaslin2(

input_data = PRE,

input_metadata = sam_16S_PRE,

normalization = “CLR”,

transform = “None”,

output = “maaslin_PRE_output”,

fixed_effects = “SubjectID”,

)

#this works

maaslin_res ← Maaslin2(

input_data = PRE,

input_metadata = sam_16S_PRE,

normalization = “CLR”,

transform = “None”,

output = “maaslin_PRE_output”,

fixed_effects = c(“Time.Point”),

)

#does not work

maaslin_res ← Maaslin2(

input_data = PRE,

input_metadata = sam_16S_PRE,

normalization = “CLR”,

transform = “None”,

output = “maaslin_PRE_output”,

fixed_effects = c(“Time.Point”),

random_effects = c(“SubjectID”)

)

I tried the example from the tutorial and the same problem occurs using the random effects

#this works

fit_data ← Maaslin2(

input_data, input_metadata,‘demo_output’, transform = “AST”,

fixed_effects = c(‘diagnosis’, ‘dysbiosisnonIBD’,‘dysbiosisUC’,‘dysbiosisCD’, ‘antibiotics’, ‘age’),

normalization = ‘NONE’,

reference = ‘diagnosis,nonIBD’,

standardize = FALSE)

#does not work

fit_data ← Maaslin2(

input_data, input_metadata,‘demo_output’, transform = “AST”,

fixed_effects = c(‘diagnosis’, ‘dysbiosisnonIBD’,‘dysbiosisUC’,‘dysbiosisCD’, ‘antibiotics’, ‘age’),

random_effects = c(‘site’, ‘subject’),

normalization = ‘NONE’,

reference = ‘diagnosis,nonIBD’,

standardize = FALSE)

I have tried restarting R studio and reinstalling Maaslin2. Neither have resolved the issue. What is especially strange as I have been working with these data for weeks and the models with random effects have worked as expected. I do not think the problem is with my data because the example also does not run when random effects are included.

P.S. I know including example data and reproducible code would be useful, but I am relatively new to the forum and unsure how to do so. I am willing to include it if someone can point out how to include it in the post.

Thank you!