Fig. 3: Deconvolution of immune cell types on Illumina 450 K array.

a Matrix of marker CpGs (n = 600) used for building immune cell methylation reference of 450 K data. Samples for six cell types were included: neutrophil (n = 15), natural killer cell (n = 6), B-cell (n = 4), CD4+ T-cell (n = 6), CD8+ T-cell (n = 5) and monocyte (n = 5). b Deconvolution accuracy represented as boxplots showing accuracy scores for the different deconvolution methods, normalization methods, and cell types on 200 in silico mixtures. Black diamond shapes represent median values, colors represent cell types. The boxplots present median values and quartiles, whiskers the minimum and maximum values, and dots the individual data points. P-values were determined using two-tailed FDR-adjusted Dunn’s tests. *P < 0.05, **P < 0.01, ***P < 0.001. c Scatter plots showing true proportions (x-axis) and predicted proportions (y-axis) in percentages for the best-performing (left-upper) and worst-performing (right-lower) algorithm-normalization combinations on 200 in silico mixtures. R² and p-values were calculated using Spearman’s rank correlation test. d Performance of deconvolution on 200 in silico mixtures for all algorithm-normalization combinations represented as circles. Spearman’s R² is represented by color, root mean squared error is represented by size. Rows show deconvolution algorithms, columns show normalization methods. e Scatter plots showing true proportions (x-axis) and predicted proportions (y-axis) in percentages for the best-performing (left-upper) and worst-performing (right-lower) algorithm-normalization combinations on 12 in vitro mixtures. R² and p-values were calculated using Spearman’s rank correlation test. f Scatter plots showing true proportions (x-axis) and predicted proportions (y-axis) in percentages for the best-performing (left-upper) and worst-performing (right-lower) algorithm-normalization combinations on five FACS-sorted whole-blood samples. R² and p-values were calculated using Spearman’s rank correlation test. ‘X’ symbol represents missing values. Source data are provided as a Source Data file. Exact p-values are added in the Source Data file.