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.
Thanks for bringing this to our attention. I believe this is a bug when running Maaslin2 using the "LOG" transformation (the default). Maaslin2 adds a pseudo count before taking log transformation to accommodate zeros, which causes it to count non-zero values incorrectly. I’ll report this to the developers.
Thank you for the reply! I just also wanted to add that I got the N.not.0 error (as well incorrect significant results/incorrect figures/incorrect Y axis on my figures) when running it on R-4.0.2. but did not get the same problem when running the code on R-3.6.0. When using R-3.6.0 the output I get using the demo Maaslin2 tutorial data is all correct. I’m not how, but the problem may have something to do with the version of R installing and running MaAslin2.