Confusion over factors of the "value" column in significant_results.tsv

Hi,

I have been running Maaslin for a while and the values in my “value” column from the significant_results.tsv were always the different factors of the column. Recently, for some reason, the values are now changed to 1, 2, 3… instead. I don’t know what the values 1, 2, 3 represent. I reran the code from before (where I got the actual names of my factors), however, am still getting this issue.

For example, this is an example of my code:

fit_data = Maaslin2(
input_data = input_data,
input_metadata = input_metadata,
normalization = “CSS”,
standardize = FALSE ,
transform = “NONE”,
analysis_method = “NEGBIN” ,
max_significance = 0.05,
output = “xxx”,
fixed_effects = c(“Sample”),
correction = “BH”,
reference = c(“Sample,aaa”),
min_abundance = 0,
min_prevalence = 0,
heatmap = TRUE,
plot_scatter = TRUE)

My four factors in Sample are aaa, bbb, ccc, ddd. aaa is my reference.

In the past, the “value” column of the significant_results.tsv would be:

value
bbb
bbb
ccc
ddd
bbb
ccc

Now, when I run Maaslin2, the value i get is:

value
2
2
3
4
2
3

Is there something I can change to return to bbb, ccc, ddd instead of 2, 3, 4?

I hope my explanation isn’t confusing! Thank you for the great tool!

Carmen