I see. Thanks a lot for the response, Sun-Gou! I learned that in the “normalized” ROS/MAP data on Synapse, the batches of plates 1–6 and plates 7–8 were batch corrected separately for individual plates (e.g. plates 1–6 and 7–8 respectively), but not across all plates. I think that’s why plates 7–8 can still be separated from plates 1–6 in the PC1-PC2 plot. I think I should correct one more time for all plates using the normalized data.