Hi there,

I have performed two PCA analysis on two different data sets, consisting of the analysis of different proprieties of the same samples.

I got what I was expecting, some samples are cluster together and away from others. However I also noticed that the scale of the PCA axis is quite different, on the left the range is much smaller compare to the PCA on the right, for both the x and y axis. How should I interpret this? Can I say that for the measurement Y there are more variations (and bigger fold change) among the different sample? Or this is due to the scale, data points, something else of the original data used for the PCA?

Thank you.

Why would you expect that the scales would be the same? They're different variables accounting for a different amount of the variance in that data set. The magnitude of the variance itself between 2 variables isn't really comparable.