Prediction accuracy of sample-level cell-type expression by approach.

For each cell type, genes common across approaches were used. No. common genes are 3837 for CD4, 6274 for CD8, 5185 for CD14, and 2689 for CD19, respectively. (A) Pearson correlation and (B) log root mean square error (RMSE) comparing observed to predicted cell-type expression of genes from the same subjects, one estimate per subject. (C) Pearson correlation and (D) log RMSE between observed and predicted cell-type expression across testing samples for each gene, estimate per gene. RMSE was standardised by the average observed expression per gene. CIBX-inbuilt: CIBERSORTx expression deconvolution with the inbuilt signature matrix; CIBX-custom: CIBERSORTx expression deconvolution with a custom signature matrix derived from sorted cell-type expression in training samples; bMIND: bMIND expression deconvolution with flow fractions; swCAM: swCAM deconvolution with flow fractions; LASSO/ridge: expression predicted from regularised multi-response Gaussian models. (PDF)