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?