Example of why we shouldn't consider non-biological zeros in differential abundance analysis

Hi all!

I have read this fantastic paper, and I wanted to prepare a presentation to share with my colleagues.

I would like to demonstrate visually that if you consider non-biological zeros in your differential abundance analysis, it can make it seem like 2 samples are spuriously similarly or differently expressed (re: this paragraph in the Jiang paper "For each taxon, we observe that the imputed abundances and the original non-zero abundances have similar ranges and both suggest that the taxon is more abundant in T2D samples than in control samples. However, this abundance difference is obscured by the prevalent zeros before imputation and thus cannot be captured by DESeq2-phyloseq.")

Essentially, I need help creating an ASV table or a figure to demonstrate this. Something like this, where the cells are relative abundances with lots of zeros (biological and non-biological). And I want to show that if you consider all zeros in the data, you could say 2 IDs have differentially expressed taxa, but if you do not consider the non-biological zeros, the 2 IDs are similar. I recall seeing such an example in a paper somewhere, but alas I cannot remember where.

Thank you!!

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Hi @sabrina_charette, I do not have anything to add to this directly, other than that I wanted to share these papers to help with your presentation narrative:

  1. Blasco-Moreno, Anabel, Marta Pérez-Casany, Pedro Puig, Maria Morante, and Eva Castells. 2019. “What Does a Zero Mean? Understanding False, Random and Structural Zeros in Ecology.” Methods in Ecology and Evolution / British Ecological Society 10 (7): 949–59. http://dx.doi.org/10.1111/2041-210x.13185

  2. Kaul, Abhishek, Siddhartha Mandal, Ori Davidov, and Shyamal D. Peddada. 2017. “Analysis of Microbiome Data in the Presence of Excess Zeros.” Frontiers in Microbiology 8 (November): 2114. http://dx.doi.org/10.3389/fmicb.2017.02114

I am sure there are quite a many more papers I'm not considering, or am aware of... Obviously, disregard if you're already aware of these. :slight_smile:


Thank you! I was not aware of these publications, so thank you for sharing!


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