I’m using MaasLin2 with abundance data, it works well for almost all my sample and I’ve results at the end. But for some column, I have this message in the console and the features seem to be completely ignored in the output:
Error in glm.fit(fr$X, fr$Y, weights = fr$wts, offset = fr$off, family = fm, : NA/NaN/Inf in 'x'. I checked and have no nan value in my input dataframe.
My Maaslin options are (i replaced some names for confidentiality):
fit_data2 = Maaslin2(
input_data = df_input_data,
input_metadata = df_input_metadata,
normalization = “NONE”,
transform = “NONE”,
analysis_method = “CPLM”,
output = “outdir”,
fixed_effects = c(“effect1”, “effect2”, “effect3”),
reference = c(“value1,value2”))
Is there something I can do ?