В Sun, 13 Oct 2024 13:19:09 +0200 David Bars <el.segarr...@gmail.com> пишет:
> Through different microbiota datasets, I have plotted PCoA, db-RDA and > sPLS-DA using 3 different types of normalization methods (Total sum of > squares, cumulative sum of squares and rarefaction). For each dataset > and multivariate analysis (PCoA, db-RDA or sPLS-DA) in order to easily > interpret if the different normalization strategies creates me > different or equivalent PCoA for example, I have calculated the > Procrustes sum of squares and the RV coefficient of co-inertia. > However, for the RV coefficient of co-inertia, I have obtained the > value 1 (perfect equivalence) for the PCoA comparisons amongst the 3 > methods of normalization, and also for the db-RDA. For the sPLS-DA I > have not obtained 1 for all the comparisons. > Why could obtain 1 for PCoA and db-RDA and not for sPLS-DA? It's hard to give a precise answer without seeing the details. For example, how exactly was sPLS-DA calculated? Isn't it a supervised _classification_ method, unlike the distance-based methods PCoA (unsupervised dimensionality reduction) and db-RDA (correlation analysis between two blocks of data)? Perhaps the reason you couldn't get an RV coefficient of exactly 1 for sPLS-DA with different scalings is because the method is sparse, i.e., it sacrifices some of its ability to explain the data in order to obtain loadings that are exactly 0 for "unimportant" variables. Different scalings may have resulted in different subsets of related variables passing the "importance" threshold. -- Best regards, Ivan ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide https://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
