Fig. 6

(Top) Distributions of Spearman correlations for gene-gene pairs subject to four data transforms: log transformed TPM (abbreviated as TPM), log transformed TPM with shift(abbreviated as TPM-shifted), local leveled (LL), and nonlinear rescaled (NL). The different data transforms are explained in Sections "Bias detection and characterization" and "Bias correction". For comparative purposes, the correlation distribution for data which shuffles the per-gene expression levels among patients is also shown. (Bottom) Distributions of differences between pair-by-pair correlations computed using the different transforms: TPM minus NL, TPM-shifted minus NL, and LL minus NL