Differential Abundance Methods & Quality

Hi @jwdebelius

Many thanks for your response, this is helpful. Really grateful :slight_smile:

Feel free to split this into a different query ticket as I am not sure.

Regarding the differential and relative abundance, I have seen some papers run kruskal wallis test (more than 2 groups) or Mann Whitney (2 groups) on the relative abundance data results and consider this as differential abundance while others use ANCOM for differential abundance. Do you think there is any difference and can we argue that both could be called differential abundance?

Kind regards
Marwa

Hi @MarwaTawfik,

I did move ths to a new topic, because I think this is separate.

There's a pretty wealthy literature on this topic. I'd recommend looking at a few of these papers which address your question around MW/KW, ANCOM, and others.

I think the first comparison of ANCOM and KW was by Weiss et al

And then it was re-visited by Lin and Peddada in 2020:

https://www.nature.com/articles/s41522-020-00160-w

Best,
Justine

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Wow, Lin and Peddada in 2020 is a great find, partly because it covers almost all the common methods used:

Cumulative-Sum Scaling (CSS) implemented in metagenomeSeq, Median (MED) in DESeq2, Upper Quartile (UQ) and Trimmed Mean of M-values (TMM) in edgeR and Wrench, and Total-Sum Scaling (TSS) (relative abundance). ... “ELib-UQ” (Effective library size using UQ) and “ELib-TMM” (Effective library size using TMM)

ANCOM, ANCOM-BC, LEfSe, gneiss18, phylofactorization61,62, PhILR63, and selbal64

It's all in there!

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Hi @jwdebelius
Thanks again.
According to this paper they mentioned running Kruskal–Wallis test on the rarefied samples for differential abundance. Have you heard or have you seen it run on unrarefied samples?

Hi @MarwaTawfik,

I think the point of this paper and much of the recent literature is that it is not appropriate for the data. It ignores some basic assumptions around the distribution and structure.

Are there situations in which you might structure your data in such a way that it could be passed into a test that assumes normality? Absolutely, tools like ANCOM, Aldex2, Gneiss, and Phylofactor are all built on those types of transforms.

There are certainly other papers that evaluate KW or other techniques on other transforms. I dont have the exhaustive literature of how everyone has compared all their methods.

I will, however, mention that I'm putting together slides for a class discussion about this topic, and I'll share my first slide:

Best,
Justine

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