ANCOM more/less abundant taxa

[Nicholas_Bokulich]

Hi @1112,
Sorry for the delayed response.

@1112

To my understanding, the output first table shows the features that reject the null hypothesis, which means that they are differentially abundant

Correct

@1112

The second table shows the percentile of the features in different groups. Are these numbers the number of reads of those features?

Yes. See this explanation of the percentile abundance results.

@1112

does the difference in library sizes between the samples/groups (e.g. 3x - 10x difference) affect the interpretation of the percentile as more/less abundant because they are not normalized?

These frequencies are not normalized in the percentile abundances table; however, they are normalized by ANCOM prior to calculating significance so should not influence the results/interpretation.

@1112

the second table shows a higher abundance of the feature in control but the volcano plot gives a negative clr mean difference

higher in control, lower in treatment, so negative clr makes sense. As indicated in that forum post, which group is assigned as "control" can be arbitrary (maybe alphabetical order?) so I would not worry about this.

@1112

My question is how to tell which group has higher/lower abundance besides from using the percentile table in the ANCOM output?

use the percentile abundance table as a guide. In this example, that feature is very clearly more abundant in the control group.

I hope that helps!