Hi, there!
I used a transposed otu table, and sample data from phyloseq to construct a DESeq object.
However, in my otu table, there are zeros in almost each column, which prevent DESeq to do the log transform. I noticed that if I just simply add 1 to all values, I can bypass the issue. But there are several discussions indicating we shouldn't add 1 to the otu table.
I am just wondering, what will the best way to fix it then?
Thank you very much!