I am working on a gut microbiome data. I have samples before and after taking the 2 kinds of supplements. I wish to use longitudinal first difference using shannon vector. Here is my code:
qiime longitudinal pairwise-differences --m-metadata-file metadataall.txt --m-metadata-file core-metrics-results/shannon_vector.qza --p-metric shannon --p-group-column Supplement --p-state-column Session --p-state-1 1 --p-state-2 2 --p-individual-id-column person_id --o-visualization core-metrics-results/pairwise-differences_group_supplement.qzv
I have 2 questions:
- In the metadata file, there are 2 rows for each person as there are 2 samples before and after. So there is a repetition of the person id. The documentation of qiime says it takes only one ID and ignores the other by default. Can someone explain me this?
- Is there a better way to compare the relative difference[after-before] of 2 groups of people?