Maaslin2 q-values are same

Downstream analysis and statistics MaAsLin
1

Hi, I am running Maaslin2 in R with these commands -

fit_func = Maaslin2(input_data = k_data,
input_metadata = k_meta,
output = “KEGG2”,
normalization = “NONE”,
transform = “LOG”,
fixed_effects = c(“source”),
analysis_method = “LM”,
plot_heatmap = TRUE,
min_abundance = 0.0,
min_prevalence = 0.1)

However, looking at the significant results, I realized that my q-values are the same in 7 out of the 8 associations. My goal is to find differentially abundant KOgenes between 2 environments - Wild and Farm. Additionally, my data run in humann3 and normalized to relative abundance.

Below are what my data looks like.

Data -
Kegg_relab_mas.tsv (638.4 KB)

metadata-
Kegg_relab_meta_mas.tsv (203 Bytes)

significant features table-
significant_results.tsv (831 Bytes)

Any idea why my q-values are the same?

Any help will really be appreciated!.

Thank you.

2

Hi @OluchiAroh

This is an expected behavior given the way FDR corrected p-values are calculated. You can find more information on them here:

https://www.jstor.org/stable/2346101

Cheers,
Jacob