Table 3 Number of eGenes and replication of eQTL for the different aggregation and normalization strategies in Smart-Seq2 iPSC cells. The same set of 12,720 genes were considered in all of the strategies. Discovery FDR was controlled at 5% for the discovery; replication was defined as FDR < 10% and consistent direction of effect in the two bulk studies, i.e., matched bulk (N = 87, m-bulk) and all bulk set (N = 526, a-bulk)
From: Optimizing expression quantitative trait locus mapping workflows for single-cell studies
| Â | Discovery (FDR 5%) | m-bulk (FDR 10%) | a-bulk (FDR 10%) | |||
|---|---|---|---|---|---|---|
eGenes | % tested | # replicated | % replicated | # replicated | % replicated | |
dr-mean | 1835 | 14.43% | 889 | 48.45% | 1367 | 74.50% |
dr-median | 1337 | 10.51% | 650 | 48.62% | 952 | 71.20% |
dr-sum | 1463 | 11.50% | 819 | 55.98% | 1153 | 78.81% |
d-mean | 1305 | 10.26% | 768 | 58.85% | 1046 | 80.15% |
d-median | 776 | 6.10% | 470 | 60.57% | 625 | 80.54% |
d-sum | 1174 | 9.23% | 709 | 60.39% | 951 | 81.01% |
m-bulk | 2590 | 20.36% | – | – | 2448 | 94.52% |