I want to use deseq2 for differential abundance analysis for 16s amplicon data analysis.
I do have three tissue:
summary(sample_data(physeq)$Tissue) Leaf Root Soil
And each tissue has given 3 treatment.
summary(sample_data(physeq)$Treatment) T1 T2 T3
Now I just want to use soil data and want to see the effect of treatment T1, T2 and T3 on microbial abundance in soil only.
for this how should I should I take only soil sample from physeq data and modify the below condition code.
diagdds = phyloseq_to_deseq2(kostic, ~ DIAGNOSIS)
I will be very thankful for your help.
Kind Regards Yogesh