Fig. 3.

Methods to assess overall infiltration. a Matrix plot of Spearman’s correlations for the methods providing information on overall immune infiltration; tumor infiltrating lymphocytes (TILs) or the sum of T cells and B cells was taken to derive a TIL fraction. b Matrix plot for Spearman’s correlations of the methods providing information on overall immune infiltration in ER-positive tumors and c ER-negative tumors. aCBS, absolute CIBERSORT [20]; digTMA, tissue microarray scored by Visiopharm (digital analysis); MCP, MCP-counter [22]; meTIL, methylation TIL score [27]; metCBS, methylCIBERSORT [25]; itTIL, intra-tumoral TIL on H&E; qSEQ, quanTIseq [21]; sTIL, stromal TIL on H&E; TILrna, TIL score based on transcriptome [26]; TMA (H&E), sTIL scored on TMA; TMA (IHC), tissue microarray scored by pathologists with CD3 and CD20 markers to calculate the sTIL; WS (IHC), whole slide immunohistochemistry of CD3 and CD20 by pathologists