Fig. 4

Gene expression variation associated with smoking status, specimen collection timing, cohort and inhaled medication. PCA was performed using scaled normalized (VST) expression data for a 17,954 genes from all subjects in the smoking index training set (N = 1578); b and c 17,954 genes from within-indication subjects in the training set (N = 311); d 998 benign vs malignant DE genes from within-indication subjects in the training set (N = 311). e Distribution of basal, blood, cilia and immune cell type indexes in within-indication subjects in the training set, separate by specimen collection timing