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Aug 28, 2017 at 13:42 comment added Krrr I would expect the bottom right plot to be the same as with the original data clustering plot at top right but it is not.
Aug 28, 2017 at 13:40 comment added user166243 your question is: "should all analysis (e.g. k-means) be run on the m PCA scores instead of the d dimensional data". But in those plots, I see that the clusters are exactly the same for clustering on original data and pc's. This is also what is predicted by the theory. So what is the question still?
Aug 28, 2017 at 13:16 comment added Krrr thanks for your answer. I have edited the question with some R code and plots, perhaps the question make more sense now?
Aug 28, 2017 at 12:50 history answered user166243 CC BY-SA 3.0