I do have the multiple soil samples and I have given three treatment to these soil sample: T1, T2, T3. So I want to see the treatment effect on microbial abundance in these samples.
#[sample metadata columns are like this:
sample_id Tissue Treatment Villages Region
soil-01 soil T1 Menjana Rajshahi
soil-02 soil T2 Khola Mymensing
could you please suggest me how I can design --p-formula for this analysis:
Initially, I run all samples together: I do have 3 tissue: root, shoot and soil and three treatments: T1 , T2 ,T3.
For gneiss differential abundance, I only processed with soil samples with filtering the data, but earlier diversity analysis were performed all together.
should I filter the soil sample and perform the diversity analysis again? for gneiss analysis I also perform feature table filtering, should I do same filtering before doing diversity analysis.