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I have some data that I want to do a PCA plot on. However, the first two principal components are entirely due to 3 outlier samples (out of 32), and I’d like to skip these and just plot principal components starting from the 3rd. Is this possible, or would I have to do some calculations to subtract the first two principal components from the data and then plot the remainders?
If outliers are dominating your pca, and you don’t want this I would highly recommend removing them before performing your pca.