I have three different groups. I did a PCA and plotted PCA1 and PCA2 as a scatter. One of the groups looks different to the others. However, afterwards I realised that I applied PCA to each group separately, when it should be applied to all at the same time. If I apply to all at the same time, the groups look the same in the PCA plot - i.e. the blue is aligned with the red and green.

Is there any possible value in applying PCA separately and the difference found here, or is this simply a random effect of incorrect application of PCA?


1 Answer 1


It depends on your question : do you want to find the population's factorial structure (assuming all groups came from the same population) or compare the groups' factorial structure. Doing PCA, a exploratory analysis, could be more related to the first option, so you should pool all groups in a single PCA. For the second option, you could use a single factor analysis including multigroup analysis, like multigroup PCA.

There is many options available to you. Your research question should guide you.


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