![]() If that’s all Legendre^2 has to say on the matter, then I think that implies that PCoA of Bray-Curtis dissimilarities is not in itself problematic, only that the eigenvalues may need to be adjusted to properly interpret: I am also not aware that it is inadmissable to use dissimilarities (rather than distances) as input to PCoA… according to Legendre, using non-Euclidean dissimilarity matrices (e.g., with Bray-Curtis) could merely lead to negative eigenvalues, and that Legendre + Legendre recommend some procedures to correct negative eigenvalues if they are giving you indigestion. Wouldn’t then calculating the PCoA from the resulting matrix be inadmissible or least subject to uninterpretable results, given that the Bray-Curtis dissimilarity is only a true distance if calculated on relative abundance and would violate the triangle inequality when calculated on count data? description="Compute Bray-Curtis dissimilarity for each sample in a ".Thanks at pdist is looks like the Bray Curtis distance between samples u and v is calculated by: Sorry this is a bit long winded, in summary, for commands in the Diversity plug-in that return various distances using FeatureTable[Frequency) as input, are the data transformations required for each distance wrapped into the function? If so, is there a command (or set of commands) that will calculate the distance with no pre-transformation (input transformed data). I re-imported the data into qiime and coerced it into the FeatureTable semantic type and the command runs fine, but I’m not convinced it’s not doing additional transformations prior to Bray-Curtis and weighted unifrac (I’m assuming it is converting to presence/absence for Jaccard and unweighed unifrac). I have been performing a custom transformation (version of the Hellinger) and would like to calculate Jaccard, Bray-Curtis, and weighted and unweighted unifrac on that data. For Bray-Curtis, if a PCoA is being calculated, I’m assuming that the FeatureTable is converted to at least abundance data, as Bra圜urtis on count data would violate the triangle inequality (and when Bray Curtis is calculated on abundance data it becomes analogous to the L1 distance?)įor the qiime diversity beta option, possible distance metrics also include the Aitchison (I’m assuming the clr or ilr is calculated on the FeatureTable first), among several others. My understanding is that for both Jaccard and unweighted unifrac, the input feature table would be converted to presence/absence data first. It also looks like 'FeatureTable` is used as input. In qiime diversity core-metrics-phylogenetic it looks like weighted and unweighted unifrac distances are calculated along with Bray-Curtis and Jaccard and then PCoA matrices of each. I’m unsure what data transformations are being calculated prior to the distance matrix generation.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |