Calculating significantly differentially expressed genes by Z-score threshold (90th, 95th, and 99th percentile). No weighting during averaging (unlike Connectivity Map level 5 data, which weights correlated replicates higher).

Averaging per ligand

16 ligands, ‘landmark’ genes only

295 ligands, ‘landmark’ genes only

Example plot to clarify what “averaging per ligand” means:

Averaging per cell line

16 ligands, ‘landmark’ genes only

## Error in DE_heatmap(meanZ_ct, FDR_ct, pDE_ct, "Cell lines", aCut = 0.1) : 
##   Less than two samples reached FDR threshold of 10%

295 ligands, ‘landmark’ genes only

Averaging within each ligand per cell line

16 ligands, ‘landmark’ genes only

295 ligands, ‘landmark’ genes only

Comparing DE count distributions

The * denotes p < 2.2e-16 from the Wilcoxon rank-sum test comparing to averaging by ligand.