Fig. 2

Validation of quanTIseq using tumor RNA-seq data and IF/IHC images. Comparison of quanTIseq cell fractions with those inferred for IF/IHC images from melanoma (a), lung cancer (b), and colorectal cancer (c) patients. Deconvolution performance was assessed with Pearson’s correlation (r) and root-mean-square error (RMSE) considering image cell fractions (ratio of positive cells to total nuclei) as ground truth. The line represents the linear fit. d Performance of quanTIseq and previous computational methods obtained on the three validation cohorts: melanoma, lung cancer, and colorectal cancer patients. Methods performance was quantified using Pearson’s correlation (r) considering image cell fractions as ground truth. Correlations for single cell types are displayed as dots, together with whiskers and horizontal bands representing median and 95% confidence intervals. Missing cell types are visualized as triangles at the bottom of the plots. Diamonds indicate the overall correlation obtained considering all cell types together; not shown for marker-based methods, which do not allow intra-sample comparison. B, B cells. CD4, total CD4⁺ T cells (including also CD4⁺ regulatory T cells); CD8, CD8⁺ T cells; M2, M2 macrophages; T, Treg: regulatory T cells