Fig. 4

Determining K with PCA scree plot. To choose K, we recommend to use Cattell’s rule, calculating the estimated K as K = PCs + 1. The number of PCs chosen by the Cattel’s rule is shown with an arrow. The D matrix was simulated with the following parameters: n = 100, α₀ = 1, ε = 0.2, G = 1 and K = 3 (a and c) and n = 100, α0 = 1, ε = 0.2, G = 1 and K = 5 (b and d). a, b Scree plot of PCA applied on D matrix before removal of confounding probes (23,381 probes). c, d Scree plot of PCA applied on D matrix after removal of confounding probes (22,551 probes in C, 22,532 probes in d)