ANCOMBC - Clarifying Questions

Hi,
I am trying out ANCOMBC and really like this new plugin. I have some questions about how to use this plugin properly; I've read the paper but still need to absorb it.
I am running the following command:
qiime composition ancombc
--i-table fecal-table-l7.qza
--m-metadata-file Health.Merged.Metadata.V7.txt
--p-formula 'sex_spayed_neutered' \ ###this is a 4-level category: female, male, neutered male, spayed female
--p-p-adj-method 'BY' \
--o-differentials ancombc-spay-l7-fecal.qza
qiime composition da-barplot
--i-data ancombc-spay-l7-fecal.qza
--p-significance-threshold 0.1
--o-visualization da-barplot-spay-l7-fecal.qzv

Question: the output gives three plots, appearing to have chosen "female" as the reference category and presenting LFCs relative to that category.
Does this plugin support doing all of the comparisons in a single command, or do I need to set the reference separately for each analysis, and somehow accommodate an FDR control? I have significant beta diversity differences between groups using multiple metrics, so I am somewhat comfortable comparing each group to each other.
I see in the R package for ANCOMBC-2 there's support for this with FDR control across all of those comparisons, but I am not so good at R. Is there functionality for this in Qiime2?

Thank you!

1 Like

Hello and Welcome to the forum!

Unfortunately, pairwise comparisons are not implemented in Qiime2. You can provide the reference and compare all the groups to that reference. Also, I don't think that it is appropriate to perform multiple runs and then just correct p-values (I had the same idea).

Please check this comment. By the link there you can find detailed R tutorial for ancombc2, including pairwise mode.

Best,

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