Table 2 Cleaning data with high sequencing depth [23]
From: Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes
Cleaning method | #DEGs*(DEGs30&) | #DEGs/p-value | ||||
|---|---|---|---|---|---|---|
Single-organism process | Biological regulation | Regulation of biological process | Multicellular organism process | Response to stimulus | ||
Author’s$ | 130 (29) | 27/9.3e-3 | 24/2.3e-2 | 21/1.6e-1 | 21/1.9e-3 | 21/8.2e-3 |
Raw data | 135 (96) | 65/3.9e-2 | 52/3.4e-1 | 47/6.0e-1 | 7/9.4e-1 | 40/3.3e-1 |
RNAdeNoise | 336 (328) | 193/1.7e-4 | 164/5.4e-3 | 155/1.6e-2 | 33/3.1e-1 | 134/6.3e-4 |
HTSFilter | 27 (27) | 20/1.2e-1 | 14/7.4e-1 | 10/9.8e-1 | 13/1.8e-1 | 10/7.9e-1 |
counts > 3 | 184 (96) | 65/3.9e-2 | 52/3.4e-1 | 47/6.0e-1 | 38/2.1e-1 | 40/3.3e-1 |
counts > 5 | 250 (98) | 67/3.1e-2 | 54/2.8e-1 | 49/5.3e-1 | 40/1.5e-1 | 42/2.5e-1 |
counts > 10 | 572 (128) | 76/5.1e-2 | 63/2.2e-1 | 58/4.0e-1 | 11/7.4e-1 | 52/6.8e-2 |
FPKM > 0.3 | 550 (166) | 108/2.7e-2 | 91/1.1e-1 | 85/2.2e-1 | 15/8.0e-1 | 69/1.8e-1 |