UMI-count modeling and differential expression analysis for single-cell RNA sequencing

Table 6 FDRs with and without controlling batch covariates

Simulation based on data: CEL-Seq2 (both batch A and batch B) from Ziegenhain et al. [12]. Sample size was 60 (30 cells in each group). In total, Replicate A had 30 cells and Replicate B had 35 cells after QC. Group 1 had 9 cells from Replicate A and 21 cells from Replicate B. Group 2 had 18 cells from Replicate A and 12 cells from Replicate B. Method names with plateCov indicate adjusting the batch covariates. NBID_scran and NBID_scran_plateCov used the size factor computed by scran as the offset instead of the total UMI counts
Bold values indicate FDR > 0.05
Bold and underlined values indicate FDR > 0.1

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