ANCOM abundance table: more abundant in which treatment?

[colinbrislawn (Colin J Brislawn)]

Hello again,

@xchromosome

t-tests weren’t really suitable for comparing relative abundances like you would generate from microbiome analysis, and that that was the advantage that ANCOM had over them.

Good point! Compositional data has its own issues that can violate expectations of some tests. So let's dive into these new ANCOM results.

Here's how Jamie describes the ANCOM volcano plot:

@mortonjt

For the volcano plot, you are looking at the W statistic on the y-axis, and the F-score on the x-axis. So basically the x-axis is summarizing the effect size difference of the given species between your treatment groups, and the y-axis is the strength of the ANCOM test statistic.

What you want to get out of this sort of plot are the ASVs with a high F-score and a high W-statistic – in other words points that are close to the the top right corner. These indicate that an ASV is suspected to be truly different across the groups.

You have no points your top right corner... meaning that nothing is super different between groups.

Have you tried this test using all your features without grouping them at a higher taxa level? Grouping can hide cool trends of specific microbes, so performing this test yet a third time using all feature might work well.

Colin