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Table 2 Number of DE genes detected by edgeR at a FDR of 5 % in each data set, using the size factor estimates from different methods for normalization

From: Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

Method Brain   inDrop
  Total Down Up   Total Down Up
DEseq 5073 894 4179   497 298 199
TMM 4489 1051 3438   462 239 223
Library size 4258 1176 3082   492 199 293
Deconvolution 3632 1706 1926   489 212 277
shared with DESeq 2820 894 1926   411 212 199
shared with TMM 2977 1051 1926   435 212 223
shared with library size 3102 1176 1926   475 198 277
  1. This is also separated into the number of up- and downregulated genes for each data set. Upregulation refers to increased expression in pyramidal CA1 cells over oligodendrocytes in the brain data, and to increased expression after LIF withdrawal in the inDrop data. The number of DE genes shared between analyses using deconvolution and each other method is also shown
  2. DE differentially expressed, FDR false discovery rate, LIF leukemia inhibitory factor, TMM trimmed mean of M values