Can I use DESEQ2 for differential abundance analysis between two groups of samples without replicates

[markgonzalo (mark)]

I have microbiome amplicon data for two groups of samples, one group consist of 100 patients and the other are 100 normal people. I have no replicates for any individual. Can I use DESEQ2 to detect differential abundant taxa between these two groups of samples, just like LeFSe?

[salias (Sergio Alías-Segura)]

Hello!

Yes, you technically can, but maybe this is not the best approach for differential abundance in microbiome data. ANCOM and ANCOM-BC, for example, are in my opinion more suitable due to the corrections/assumptions they have. If you are interested, here you have a couple of forum posts that you may find helpful on this topic:

DESeq2 vs. ANCOM results

Hi, I have performed DESeq2 on my data, and the results seem to differ from that of ANCOM very much. For example, in case of ANCOM, I found 3 features to be differentially abundant, while DESeq identified over a hundred! I was wondering why the results seem to be so drastically different?

Differential Abundance Methods & Quality

Hi @jwdebelius Many thanks for your response, this is helpful. Really grateful 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 ar…

Cheers!