I am working on a human gut microbiome data and its association with few outcomes. Firstly, I started with PCA, and then selected 3 principal components (using this code:
modeling <- data.frame(MyResult.spca$x[,1:3], df3)) and the variables present in each component. Later, I ran regression analyses with the outcomes and 3 principal components individually, and for all variables selected in each component, adjusting for potential confounders.
However, because PCA is not discriminatory, the microbes selected at this stage were not really related to any of our outcomes.
Therefore, we went forward to perform sPLS-DA, and selected 3 components and the variables present in each component. I repeated the regression analyses for all variables selected in the components, but I am not able to select the data from components as I could do from PCA. Is there a method by which I could extract the components from sPLS-DA and run regression on it?