Hi, thank you for the great package & forum! I am new to mixOmics and would like to use the SPLS-DA vignette to analyze the impact of two different antibiotics on the gut microbiome. I have followed the tutorial (tumour case study) and replicated the same analysis to my own dataset.
With a dataset of 132 samples and 162 taxonomic features, I performed performance evaluation where ncomp = 3 seems reasonable.
Next, for the optimal number of variables to include, I ran the “tune.splsda” command (with ncomp = 3, dist = “max.dist”), and 7, 90, and 100 variables are recommended for each of the components.
Now - it’s the last bit that I’m not sure:
Has anyone seen a comp1 value that’s smaller than comp2? It may be totally OK, but I’ve never seen this in PCA-type plots, where the first component always explains the most variation. If anyone has any insight or recommendation to further diagnose the data, it’d be much appreciated.
Thanks in advance!