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Table 5 Inclusion of random effect to increase discovery power of sc-eQTL mapping in Smart-Seq2 iPSC scRNA-seq data. Shown are the number of eGenes that are discovered at an FDR of 5% and the replication in all bulk (a-bulk) defined as FDR < 10% and same sign. Tested are the expressed genes on chromosome 2 matched between the two considered aggregations (d-mean and dr-mean, n genes = 20,334)

From: Optimizing expression quantitative trait locus mapping workflows for single-cell studies

  Random effect matrix Discovery a-bulk replication
kinship 1/#cells 1/#reads eGenes % tested # replicated % replicated
d-mean 1415 6.96% 1086 76.75%
d-mean 1652 8.12% 1251 75.73%
d-mean 1645 8.09% 1233 74.95%
dr-mean 2073 10.19% 1466 70.72%
dr-mean 2750 13.52% 1832 66.62%
dr-mean 2458 12.09% 1676 68.19%