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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL)

Fig. 4

Results obtained from applying the optimal IDOL library to the testing sets. a Stacked bar plots showing the cell type fractions for each testing set sample. b Scatter plots of the true reconstructed mixture fractions (x-axes) and the predicted cell fractions obtained using the optimized IDOL library (y-axes). Circles indicate Method A samples and squares indicate Method B samples. Dotted lines indicate the line of unity and colored lines represent the regression line fit to the true reconstructed mixture fractions and predicted cell fractions. c Box plots showing the predicted cell (%) − observed cell (%) across leukocyte cell types, where blue boxes represent estimates obtained from the optimal IDOL library and red boxes represent estimates obtained from the EstimateCellCounts library. (d, top panel) Estimated false discovery rate (FDR) for a two-group comparison of DNA methylation as a function of the dissimilarity in the cellular distribution between groups (x-axes). Colored lines represent different approaches for cell composition adjustment. (d, bottom panel) Difference in the FDR between the EstimateCellCounts and IDOL libraries where points above the dotted line indicate that the EstimateCellCounts library resulted in more false positive results compared to the IDOL library. e Mean difference in the FDR for varying sample sizes when cell mixture was adjusted using cell fractions estimates from the EstimateCellCounts and IDOL libraries. Bars represent the 95 % bootstrap confidence intervals for each point estimate. Points to the right of the dotted line indicate that the EstimateCellCounts library resulted in more false positive results compared to the IDOL librarys

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