Hello, I am trying to test for changes in prevalence of species at 2 time points. I have tried several iterations of the code and I keep getting the error message Error in maaslin_fit(filtered_data, transformed_data, standardized_metadata, :
object ‘fit_data_abundance’ not found. It appears to be producing the feature tables and then goes through all of the model fitting, but then I get this error message. I don’t believe there is anything wrong with the format of my input data as I have tried running it in Maaslin2 and that works fine. The code I am using is below. Could you please assist with troubleshooting? Many thanks
maaslin3(
input_data = taxa_maaslin,
input_metadata = metadata_filtered,
output = ‘maaslin3_time_no_confounders_LOG_refwk1_11_minprevTEST’, # output directory name
min_abundance = 0,
min_prevalence = 0.05,
transform = ‘LOG’,
warn_prevalence = ‘FALSE’,
normalization = ‘NONE’,
evaluate_only = ‘prevalence’,
random_effects = ‘PID’,
fixed_effects = c(‘Week’),
reference = ‘1’, # Set reference level of Week to “1”
correction = ‘BH’
)
Hi @Katb ,
We are currently investigating what’s going on here.
In the mean time while we look at this you should adjust your parameters for:
warn_prevalence=FALSE
(no quotes around FALSE)
and
reference="Week,1"
Thanks,
Jacob Nearing
Hi @Katb,
That was a bug on our end - if you re-install with:
devtools::install_github('https://github.com/biobakery/maaslin3', ref = 'devel')
it should work now. Let me know if it’s still having issues!
Also, warn_prevalence=FALSE shouldn’t have quotes on FALSE.
Will
1 Like
Thank you so much for your help.