I am trying to analyze humann3 out pathabundance.tsv (this file was generated by joining 12 tables, not-normalized). I have 12 samples assigned to two phenotypes - resitant and suscpetible. I want to determine which pathways are more abundant in each phenotype.
fit_data = Maaslin2(input_data = input_data1,
-
input_metadata = input_metadata, -
min_prevalence = 0, -
normalization = "NONE", -
output = "demo_output", -
fixed_effects = c("Phenotype"), -
reference = c("Phenotype"))
[1] “Warning: Deleting existing log file: demo_output/maaslin2.log”
2023-06-27 13:56:08.499039 INFO::Writing function arguments to log file
2023-06-27 13:56:08.523632 INFO::Verifying options selected are valid
2023-06-27 13:56:08.526767 INFO::Determining format of input files
2023-06-27 13:56:08.52901 INFO::Input format is data samples as rows and metadata samples as rows
2023-06-27 13:56:08.562235 INFO::Formula for fixed effects: expr ~ Phenotype
2023-06-27 13:56:08.564818 INFO::Filter data based on min abundance and min prevalence
2023-06-27 13:56:08.56735 INFO::Total samples in data: 12
2023-06-27 13:56:08.569697 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2023-06-27 13:56:08.624171 INFO::Total filtered features: 0
2023-06-27 13:56:08.626819 INFO::Filtered feature names from abundance and prevalence filtering:
2023-06-27 13:56:08.694874 INFO::Total filtered features with variance filtering: 0
2023-06-27 13:56:08.697451 INFO::Filtered feature names from variance filtering:
2023-06-27 13:56:08.699565 INFO::Running selected normalization method: NONE
2023-06-27 13:56:08.702124 INFO::Applying z-score to standardize continuous metadata
2023-06-27 13:56:08.715661 INFO::Running selected transform method: LOG
Error in min(x[x > 0])/2 : non-numeric argument to binary operator
I would appreciate if you could help me troubleshoot this.
Thanks
Gurjit