Technical replicates of 6 cancer cell lines in which aliquots of the same RNA sample were subjected to replicate L1000 profiling (12 replicates in each of 3 batches, yielding 36 replicates per cell line) showed that for 88% of all pairwise comparisons of replicates, Spearman correlation was >0.9, suggesting low sample-to-sample variability (Figure S1C). Furthermore, intra-batch variation (median pairwise correlation 0.97) was comparable to inter-batch variation (median pairwise correlation 0.95), indicating high technical reproducibility.
