The bioBakery help forum

Output All results N.not.0=0

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

Hi -

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.

Best,
Siyuan

Hi Siyuan

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.

Thanks

Kind Regards
Leanne

Hi Siyuan,

I am also getting this problem in all results (not just significant ones). Was this bug fixed? What might be a workaround for fixing it?

Thanks!
Lara

Hi @Lyoon6 - my impression is that it has been fixed. Can you install the development version from GitHub and see if that changes your results?