differential abundance testing using r packages

Hi, Can anyone provide insights regarding differential abundance testing using r packages. I tired Lefse using physeq object in r package called microbiome marker, but gave a following error:

Error: Too small samples in each class or the variance of feature abundances within a class too small (zero or near zero).

I tried deseq2, by converting all by zero counts to 1 and got the results, but i was suggested Deseq2 has high rates of false postive.


Consider ANCOM-BC!
Tutorial on Github: GitHub - FrederickHuangLin/ANCOMBC: Differential abundance (DA) and correlation analyses for microbial absolute abundance data
Paper on PudMed: Analysis of compositions of microbiomes with bias correction - PMC

(ANCOM is compositional, which is good!)

There's also a Qiime2 plugin for running ANCOM:

P.S. I appreciate that you opened separate threads for separate questions.
Thanks for keeping the forums tidy! :broom: :trophy: