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
| 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 | |
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
DE differentially expressed, FDR false discovery rate, LIF leukemia inhibitory factor, TMM trimmed mean of M values