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

[carmennns2]

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

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.