Fig. 1
From: The application of epiphenotyping approaches to DNA methylation array studies of the human placenta
Principal component analysis of DNAme variation. Scree plots (A, B) show the proportion of variance explained by each principal component (PC), while heatmaps (C, D) show the R2 values of association from linear models run independently for each metadata variable (i.e., PC ~ Variable). A PC scree plot on raw data. B PC scree plot on processed, dasen + noob normalized data. C Raw data R2 heatmap showing strength of association between each PC from A and metadata variables. D Processed data R2 heatmap showing strength of association between each PC from B and metadata variables. For all plots, “SD” refers to standard deviation, “GA” refers to gestational age at birth, “Ethn” is used to denote ethnicity, P(African/Asian/European) represent the continuous probabilities from PlaNET ancestry prediction, and nRBC refers to nucleated red blood cells estimated by PlaNET. E Scatterplot of PC1 versus PC2 in the raw data, colored by cohort. F Scatterplot of PC1 versus PC2 in the processed data, colored by cohort