I am using MaAslin2 with metaphlan output from biobakery_workflow, trying to answer which bacterial abundance is associated with human gene A copy number (CN-A).
my code is very simple:
maas_CN_contin = Maaslin2( input_data = input_data, input_metadata = input_metadata, output = "CN_contin_all", fixed_effects = c("CN-Afinal"),normalization = 'NONE',min_prevalence=0.05, correction = 'BH' )
this did not give any significant result where I tried prefiltering of input_data by runnning correlation test of “each taxa (row of the input data) ~ CN-Afinal”, and retrive those have correlation test p-val < 0.05. Using this subsetted data, I got significant results.
Can you explain why this happens? -
and I went through the source code and it seems it is using glm for fitting in my case, where i am not sure how glm works with Y matrix - I saw that glm need Y as a vectorized form.