Fig. 2

In silico validation of the immune cell scoring method. a In silico validation of immune cell scores using simulated mixing proportions. RNA-Seq profiles of FACS-sorted NK cells, macrophages, CD4⁺ and CD8⁺ T cells, and non-immune CD45^– cells were mixed with known proportions to obtain a “clean” mixture. Noise was added at varying SNRs. Mixing levels were then inferred by ssGSEA from the “clean” and noisy mixtures. The Spearman correlations between the simulated and inferred levels (top panel) and the bootstrap p values for these correlation values (bottom panel) are shown on the y-axes (Additional file 1: Figure S18 and “Methods” for the calculation of the bootstrap p values). b Validation of IIS with methylation-based leukocyte fractions. Spearman correlations between the two orthogonal scores are shown on the x-axis for 13 tumor types. c Validation of TIS with TCR beta chain abundance. Both scores are computationally inferred from RNA-Seq data but employ different approaches to measure T cell levels. Spearman correlations are shown on the x-axis for 19 tumor types