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

Downstream analysis and statistics MaAsLin
1

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

2

Hi @carmennns2,

Others have also seen this issue before, apologies that you are running into it. We have had problems replicating it on our side. I do wonder if you deleted the output folder from your previous run if that solves it? If not, can you send us:

  1. R and MaAsLin versions you are using. Also the session information from the instance you are using (e.g. sessionInfo()).
  2. If possible and you are comfortable can you send us a minimally reproducible data set? If you can’t attach it here feel free to email it to me (my email is on the Huttenhower website).

Apologies you are running into this issue! We have had internal discussions about it but have yet to be able to solve which packages could be causing this issue.

Best,
Kelsey

3

Hi Kelsey,

Thank you for responding.

I managed to resolve the issue by deleting then reinstalling the package.

Thank you and have a good day,
Carmen