I am using deseq2 to find differential significant taxa (count data). The data is longitudinal and three groups of mice and I am using sth like
diagdds = phyloseq_to_deseq2(physeq.fecal, ~ condition + week_experiment +
team + condition:week_experiment)
since I have three groups, I wonder how DEseq2 is calculating the fold change and p-value !? There is neither any warning nor any error ! should I slice the data 3 different combination of each group ?!
The second question I have is about
condition:week_experiment term. I wonder how I can set it up in a way that two groups have the same initial value at the beginning (same intercept).