I am looking at various diversity metrics for three study categories (i.e “IPF”, “KTR”, “COPD”), after having performed qiime diversity core-metrics-phylogenetic.
For each of the three categories there are three sub-categories (“OW”, “BAL”, “RSB”), and I´d like to look at stratified analyses; that is for instance difference in Faiths PD alpha-diversity for “OW” between "IPF, “KTR” and “KOLS”. And then afterwards for “BAL” and so on.
However, I can not from the visualizer generated with qiime diversity alpha-group-significance categorize by more than one metadata column.
I tried making a metadata file excluding the “BAL” and “RSB” samples (thus containing 1/3 of the original metadata file), but this generated an error message related to missing samples.
There must be a (simple) way to perform analyses stratified by multiple metadata columns, sorry if this is a completely basic question.