Hi, I run the code below:
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth X
--m-metadata-file sample-metadata.tsv
--output-dir core-metrics-results
I used the same value for sampling depth, the same metadata, i ran the code 3 times without changing anything, and each time it resulted in different plots (emperor) for weighted UniFrac and unweighted
Why is that happening?
Hello!
When sampling depth X is chosen, X counts from each sample will be randomly selected for the analysis. Since this process is randomized, every time results will be a little different. So some differences in the PCoA plots are expected.
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