Fig. 3

Collective inference applied to pre-selected m=20 AMD SNPs. a–b Regularization via cross-validation. Dominant (DOM) and genotypic (GEN) models were used with logistic regression (LR), DDA PL (a), and MF (b). Independent-SNP limit is reached with λ→∞ and ε→0. Because of the pre-selection of SNPs using phenotype information, the prediction score (pseudo-AUC; pAUC) derived from 5-fold cross-validation over-estimates the true AUC. The maxima in pAUC correspond to optimal regularization. c–d Single-SNP and interaction p-values of the optimized (genotypic) model under PL (λ=0.01). The p-values from independent-SNP and pairwise tests are also shown for comparison in c and d, respectively. See Additional file 1: Table S1 for the independent-SNP results and SNP list