Table 1. Numbers of up- and down-regulated genes found using the BALF dataset and four combinations of TMM/DESeq2 normalization and edgeR/DESeq2 DEG identification and either 1 or 3 iterations.
| Normalization | Testing | Iteration | Total No. of gene | No. of DEG | No. of Upregulated gene | No. of downregulated gene |
|---|---|---|---|---|---|---|
| tmm | edger | 1 | 16,416 | 8,014 | 1,058 | 6,873 |
| tmm | deseq2 | 1 | 16,416 | 3,749 | 334 | 3,399 |
| deseq2 | edger | 1 | 16,416 | 10,166 | 810 | 9,295 |
| deseq2 | deseq2 | 1 | 16,416 | 5,875 | 136 | 5,685 |
| tmm | edger | 3 | 16,416 | 7,391 | 1,132 | 6,177 |
| tmm | deseq2 | 3 | 16,416 | 3,800 | 312 | 3,471 |
| deseq2 | edger | 3 | 16,416 | 4,057 | 1,790 | 2,231 |
| deseq2 | deseq2 | 3 | 16,416 | 4,441 | 243 | 4,146 |