I have a question regarding using microbiome dataset for DESeq2. I used DADA2 and got like 200 samples X 3000 RSVs table. I want to determine which RSV are differentially abundant across groups.
My question is that should we feed raw 3000 RSVs to DESeq2, or should we feed agglomerated RSVs (like 100~ genera by phyloseq function tax_glom()) to DESeq2? I read the vignette and find that we are to feed raw count data to DESeq2, but I have many output that differentially abundant across groups which share same genera.
Thanks in advance for help.