Using DeMixSC to deconvolve HGSC samples. (A) Boxplots showing the deconvolution performance of eight deconvolution methods for the pseudobulk and three types of bulk data in the HGSC benchmark data set. RMSE values and Spearman's correlation coefficients are calculated across 13 cell types for each sample. Smaller RMSEs or larger Spearman's correlations indicate higher accuracy in proportion estimation. (B) Distributions of DeMixSC estimated cell type proportions of Lee et al. (2020) data using consensus references. Each panel corresponds to a given cell type. (NK cells) natural killer cells, (ILC) innate lymphoid cells, (DC) dendritic cells macrophages, and (pDC) plasmacytoid dendritic cells. The P-values for Student's t-tests comparing the estimated cell type proportions across R0, ER, and PR groups are denoted as follows: (ns) not significant, P-value > 0.05; (*) P-value ≤ 0.05; (**) P-value ≤ 0.01; and (***) P-value ≤ 0.001. (C) Scatter plot comparing DeMixSC estimates of macrophages with immunofluorescent measures (CD68/CD163) in 21 HGSC samples. The black dashed line represents the diagonal, and the gray solid line indicates the linear fit across the data points.
