Differential gene expression (DGE) recovery.

Area under curve (AUC) distributions by approach and cell type (columns) for each scenario (rows). Scenarios differed in simulated dichotomous (dichPheno)/ continuous (contPheno) phenotypes, with/without sex as a covariate in the DGE analysis of the common gene sets across approaches. No. common genes are 3837 for CD4, 6274 for CD8, 5185 for CD14, and 2689 for CD19. dichPheno: dichotomous phenotype; dichPheno+sex: simulated dichotomous phenotype and sex; contPheno: continuous phenotype; contPheno+sex: continuous phenotype and sex. Each point is a simulated phenotype, and there are ten simulated phenotypes. For each simulated phenotype, the receiver operating characteristic curve and AUC were estimated by FDR fixed at 0.05 in the observed data and varied FDRs from 0 to 1 by 0.05 in the imputed data. Box plots showed the AUC distributions, with horizontal lines from the bottom to the top for 25%, 50% and 75% quantiles, respectively. CIBX-inbuilt: CIBERSORTx with the inbuilt signature matrix; CIBX-custom: CIBERSORTx with a custom signature matrix; bMIND: bMIND with flow fractions; swCAM: swCAM with flow fractions; LASSO/ridge: regularised multi-response Gaussian models. (PDF)