Table 3. The number of significant differentially expressed genes detected by each analysis method for each expression comparison.
| Analysis method | ||||||
|---|---|---|---|---|---|---|
| Comparison | J1 | J3 | DESeq2 | edgeR | limma-voom | |
| Leaf | AR/TC Early | 1050 | 642 | 934 | 754 | 774 |
| AR Middle | 1838 | 1195 | 1564 | 1450 | 1494 | |
| TC Middle | 1860 | 1290 | 1622 | 1502 | 1553 | |
| AR Late | 3762 | 3024 | 3311 | 3352 | 3497 | |
| TC Late | 2701 | 2065 | 2397 | 2334 | 2403 | |
| Root | AR/TC Early | 5 | 0 | 5 | 0 | 0 |
| AR Middle | 844 | 0 | 844 | 0 | 1 | |
| TC Middle | 186 | 1 | 186 | 4 | 1 | |
| AR Late | 3932 | 2903 | 3673 | 3344 | 3380 | |
| TC Late | 2757 | 1787 | 2622 | 2196 | 2189 | |