I am using qiime quality-control evaluate-composition to evaluate to outcome of different dada2 settings. The plugin offers the following descriptions:
–p-plot-observed-features-ratio >> observed:expected features
–p-plot-bray-curtis >> expected vs. observed Bray-Curtis dissimilarity
–p-plot-jaccard >> expected vs. observed Jaccard distances
Is it true that some measures represent ratios of obs/exp, while others calculate it in the other way (exp/obs)?
And a followup question: I assume that the Jaccard distances and Bray-Curtis dissililarities are calculated for each sample-id, and not for sample groups/replicates,etc.for the different taxonomic levels.