I do have three tissue and three treatment conditions in physeq object. My aim is to only want to use the soil sample and want to see the treatment effect on microbial abundance.
How should I remove other tissue and only retain the soil sample in
summary(sample_data(physeq)$Tissue) Leaf Root Soil
And each tissue has given 3 treatment.
summary(sample_data(physeq)$Treatment) T1 T2 T3