I do have 5 columns in metadata file: SampleID, Tissue (soil, root, shoot), Treatment (T1, T2, T3), Village and Region for all sample.
there are 3 tissue: soil, root and leaf.
I wanted to see differential abundance in all soil sample. I think I am making error in giving --P-where parameter, could you please suggest How should I correct it.
I used below command to filter and further process:
All values the grouping are the same. This method cannot operate on a grouping vector with only a single group of samples(e.g., there are no âbetweenâ variance because there is only a single group).
Debug info has been saved to /tmp/qiime2-q2cli-err-hvbdjtm7.log
This error means you donât have multiple values in the Tissue column. This makes sense, since in an earlier step, you filtered your table to only include Tissue='Soil' samples. How can you compare tissue types when you only have one type? Options include filtering your table on some other column, or computing ancom on another column.
I have given three different treatment to soil sample, so I wanted to see how T1, T2 and T3 treatment affect the microbial diversity in soil. Like this I want to repeat for root and leaf.
If you want to see how the treatment impacted differential abundance across the samples in the filtered table, specify the Treatment column when running ancom, not the Tissue column.