When I look at the output i get using Maaslin2, the column N.not.0 in the significant results file for all of my bacterial species is 0. The column is all 0 even in the file listing bacterial species which do not have significant associations with the variables I’m testing for. I do not understand why I am getting this output particularly when the input data in my taxonomy table looks normal and a good proportion of my data is not 0.
I get the same problem even when using the demo data from the Maaslin2 tutorial using the code below.
library(Maaslin2)
input_data = system.file(
“extdata”, “HMP2_taxonomy.tsv”, package=“Maaslin2”)
input_metadata = system.file(
“extdata”, “HMP2_metadata.tsv”, package=“Maaslin2”)
df_input_data = read.table(file = input_data, header = TRUE, sep = “\t”,
row.names = 1,
stringsAsFactors = FALSE)
df_input_metadata = read.table(file = input_metadata, header = TRUE, sep = “\t”,
row.names = 1,
stringsAsFactors = FALSE)
fit_data = Maaslin2(
input_data = input_data,
input_metadata = input_metadata,
output = “demo_output”,
fixed_effects = c(“diagnosis”, “dysbiosis”))
Does anyone have some insight on why this is happening?
Thank you
Anne