If there are groups selected where not all subjects are selected, then PCA is only being computed on those that are included. For example: <img width="76" alt="Image" src="https://github.com/user-attachments/assets/e38a1605-b412-4d06-8879-ec51f4a9af1b" /> <img width="364" alt="Image" src="https://github.com/user-attachments/assets/bfb01b21-4f26-419c-b46f-29aac6810ae0" /> In PCA, the "right" ones will be excluded from the PCA analysis.