Interpretation of the ANCOM plots

User Support
1

Hi,

Could you please help us with the following questions:

i) What does W represent? (I looked up the meaning of W and could not find a clear explanation).
ii) How are W and clr calculated, step-by-step (not the formula)?
iii) How can we "convert" W into a p-val or padj-val (q-val) type of measure?
iv) Can p-values be added to qiime composition ancom?

We would like to know how we can interpret it in a manner similar to volcano plots.
(running Qiime 2023.2 installed though conda).

Thank you for creating and maintaining such a critical resource !
Best,
Cori

2

Hello Cori,

Welcome to the forums! :qiime2:

ANCOM W value explained with step-by-step calculation

The W vs CLR plot is already a volcano plot, just without the color coding and explicit thresholds. You can make it look like a volcano plot using R.

If you run ANCOM directly in R, adjusted p-values are included in the out$res results data frame. These are not included in the Qiime2 output.

These questions are foundational to the ANCOM method. It may be worth revising the details of the original ANCOM-BC paper:

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