What are the missing values (black dots) after you perform a PCA?
Does your data possibly have missing values? This could cause the Prin formulas to end up resulting in missing values as well.
Regarding Summary Plots and Missing Values in Principal Components Analysis
Yes, my data has some missing values which I want to exclude. I don't think there's any other way than imputing the data.
If you wish to keep those rows for PCA, I think you will have to use imputation.
