To more extensively compare L1000 to RNA-seq, we analyzed 3,176 samples (previously sequenced by the GTEx Consortium (The GTEx Consortium, 2015)) profiled on both platforms. This analysis showed that cross-platform similarity was high (median self-correlation 0.84), with a right-shifted distribution compared to non-self correlations (Figure 1E, lower panel left). Recall analysis similarly showed that 98% of samples had a sample recall > 99% (indicating 99th percentile) (see STAR Methods). Taken together, these results indicate a strong degree of similarity of profiles across L1000 and RNA-seq platforms.
