Fig. 3

Linear modeling with bliss independence. a-b R² values show the goodness of fit of the model for the high (a) and low (b) dose assays. Median R² is 0.81, showing that the model fits well the majority of the data. Gray bars show R² values when no median polish is performed in the pre-processing of the cell line plates, showing that median polish increases R² values and probably reduce noise. c Pearson Correlation between low dose and high dose singlet viabilities across cell lines. Correlations are much higher when using the solved singlet viabilities than when using the viabilities measured on the plate. d Scatter plots of singlet viabilities between high and low dose, for measured singlets (left panels) and solved singlets (right panels). In these four examples, correlations went from negative to positive and significant. e-g R² vs other measures on models at standard drug dose. e Negative correlation between the model R²’s and the number of synergy found using an arbitrary cutoff (> 0.3) on Excess Over Bliss (showing high dose assays only). The cell line with the worst R2 also had the most synergic combinations (more than 2500 out of 5778), most of them are probably false positives. f The number of significant synergies does not correlate with the models R². g The sample variance measured from the DMSO wells is a surrogate for the experimental noise. It correlates with low R² for models with R² < 0.8; it suggests that very low R² are mainly due to noise on measurement rather than an abundance of synergism or antagonism