Hi DEICODE Devs,
Thanks for providing these tools for analyzing compositional data - they’ve been very helpful for the analysis of our environmental DNA data looking at the COI gene.
As is mentioned in the “Help understanding DEICODE” post from March 2019, it is suggested not to bin features by taxonomic assignment before running DEICODE. However, for a project I am working on, we are most interested in the species that are causing our samples to cluster into two groups on our DEICODE PCA, not the different ASVs that make up those species. We’ve run the PCA both ways (with the unmerged ASVs, and the ASVs binned at the species level), and it isn’t significantly affecting the clustering of our samples (see attached).
Would you be able to provide some more information regarding why you advise against binning by taxonomic assignment before running DEICODE? If the DEICODE RPCA is giving consistent results for unmerged ASVs and ASVs binned by species, would you take this as justification for visualizing PC loadings at the species level rather than at the ASV level to simplify this analysis?
Thanks in advance for your response!