DESeq2 (zeros in the taxa table)

Hi this is regarding DESeq2. I first created a phyloseq object from qiime2 artifacts and then subjected it to Deseq2. At one step I got a error
Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, :
every gene contains at least one zero, cannot compute log geometric means

I realised the taxa table has many zeros as many taxa are absent in Samples.
How to procced from this?? I triedreplacing zeros with 1 and again creating phyloseq object and running deseq2, I now got results

My question is : Is this a valid way to do it?
If not how to proceed further?

Hi @komal,

DeSeq2 isn't really a valid way to approach differential abundance testing. Several authors have shown that it doesn't model the data correctly whcih leads to a high rate of false positives. ANCOM-II (in R); ANCOM-BC (R or qiime2) and Aldex2 all make better assumptions about hte data and handle zeros more appropriately.

You can also think about how to filter your features to maximize information. If you have a feature in a single sample, can you perform a statistical test? How do you know what's noise and what's signal?