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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

  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%