The bioBakery help forum

Pairwise comparisons

I have a rather basic question that I’d like to check my understanding on. For comparing conditions, I have a single fixed effect with levels A, B, and C. I can run MaAsLin2 with level A as the reference and see what taxa in B and C are different from A. If I want to essentially do pairwise comparisons and also learn what taxa in B and C are different from each other, as I understand it, I would re-run the analysis with level B (or C) as the reference. Is this correct?

To correct these p-values, I would just combine these results and do the BH correction on the original p-values, yes?

Is there anything wrong with this approach? Is there a better way to go about it?

Thanks for a great tool.

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Hi Jess

I was just wondering if you have got any answers for your question? This was exactly my question.

And in this case I was just wondering how we can creat one heat map instead of multiple ones? since I have many levels!

Cheers Rogi

Hi @Jess_Jarett That’s correct. I don’t see any issue as long as the p-values are adjusted for each pairwise comparison separately (see this for a related discussion by Gordon Smyth).

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Hi @roghaieh_ashrafi - this is currently not possible with the default MaAsLin 2 workflow. However, once you get the appropriately adjusted p-values and q-values (as stated above), you can use an external package like Complexheatmap or pheatmap to create a heatmap that includes all the individual comparisons in the same figure.

All the best,

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