samples is chosen (method = maxRowVariance), (iii) if there are more than two probes, the probe with the highest connectivity (summed adjacency) is chosen (connectivityBasedCollapsing = TRUE). Based on the anatomical labels given in the AHBA, 2334 out of 3702 samples were mapped to Braak stage-related regions R1–R6 as defined by the BrainNet Europe protocol18 and each region corresponds to one or multiple anatomical structures (Supplementary Table 1). The locus coeruleus and pontine raphe nucleus are both part of the pontine tegmentum in R2.
