No abundance for several species

Downstream analysis and statistics MaAsLin
1

Hi!

I am comparing communities from two different timepoints: baseline and week 2 - I have 40 samples pr timepoint. The MaAsLin3 analysis ran well and I added a p-value cut-off = 0.05 and the small_random_effects = TRUE parameter.

I have inspected the output significant_results.tsv file and I can see that for some of the species there is only one row/entry with prevalence. There is no abundance and I wonder why and if it is something to be concerned about?

I have filtered the significant_results.tsv file according to species name and then highlighted with orange some of the species that are only represented with one row, starting from row 59:

Screenshot 2025-09-26 at 13.30.59
Screenshot 2025-09-26 at 13.30.592346×1118 507 KB

Let me know if you need more information :slight_smile: thank you!

2

Hi,

Are the rows you need in the all_results.tsv table that contains everything?

Will

3

Hi!

Yes, the rows are in the all_results.tsv:

Screenshot 2025-09-29 at 09.15.18.png1118×604 162 KB

Why are they not a part of the significant_results.tsv file? :slight_smile:

Best,

Caroline

4

The results are put in the significant_results.tsv file if they either (1) have an individual q-value that is significant or (2) have a joint q-value that is significant. In those cases, the rows that were not included had neither, though their mate was individually significant.

1 Like
5

I see! I thought the mate would always be included :slight_smile:

Thank you for the clarification and quick help!