In the following examples we see the second example has better result and more separable.
Is it possible to see somehow find this separation based on the data matrix of PCA result? e.g. based on some kind of score like Mean, Median calculation of the components or any other way?
The code used:
pca <- prcomp(dataMatrix, scale=T)
scores <- data.frame(Groups, pca$x[,1:3])
pc1.2 <- qplot(x=PC1, y=PC2, data=scores, colour=factor(Groups)) + theme(legend.position="right")
Thanks in advance