I want to report an unexpected behaviour:
pca.res <- PCA(X1, scale.unit = T, ncp = 10, graph = F)
As you can see, the mean of the pca score is not even close to 0. The mean should be 0 for standardized PCA (scale.unit = T). For now, I cannot send you the data to reproduce this for confidenciality reasons, but I can tell you that it probably has to do with the fact that some of the input variables are constant. The issue was solved when I filtered constant variables.
Perhaps a warning or an error should be raised when constant variables are found in the input matrix, I would have messed downstream analysis if I had not noticed.
Thank you in advance,