Table 4 Significant genes in all methods of Holstein milk data. Gene lists of Holstein milk data siginificant in nominal 0.005 significant level for all methods (BALLI, DESeq2, edgeR, LLI, and voom) and their p values (FDRs) are provided
BALLI | DESeq2 | edgeR | LLI | voom | |
|---|---|---|---|---|---|
SPTSSB | 4.457 × 10−4 (9.222 × 10− 1) | 2.660 × 10− 3 (9.997 × 10− 1) | 2.160 × 10− 4 (1) | 8.686 × 10− 5 (1.787 × 10− 1) | 1.037 × 10− 3 (9.999 × 10− 1) |
NOS3 | 4.676 × 10− 4 (9.222 × 10− 1) | 2.396 × 10− 4 (6.298 × 10− 1) | 2.549 × 10− 4 (1) | 8.957 × 10− 5 (1.787 × 10− 1) | 8.693 × 10− 4 (9.999 × 10− 1) |
FXYD3 | 7.198 × 10−4 (9.507 × 10− 1) | 2.813 × 10− 4 (6.298 × 10− 1) | 5.182 × 10− 4 (1) | 1.513 × 10− 4 (2.012 × 10− 1) | 2.097 × 10− 3 (9.999 × 10− 1) |
SPESP1 | 1.103 × 10− 3 (9.507 × 10− 1) | 4.834 × 10− 3 (9.997 × 10− 1) | 1.669 × 10− 3 (1) | 2.579 × 10−4 (2.385 × 10− 1) | 4.001 × 10− 3 (9.999 × 10− 1) |
CHST1 | 1.339 × 10− 3 (9.507 × 10− 1) | 8.624 × 10− 4 (9.383 × 10− 1) | 1.872 × 10− 3 (1) | 3.166 × 10− 4 (2.385 × 10− 1) | 6.108 × 10− 4 (9.999 × 10− 1) |
LEPREL1 | 1.387 × 10− 3 (9.507 × 10− 1) | 2.554 × 10− 3 (9.997 × 10− 1) | 3.297 × 10− 3 (1) | 3.334 × 10− 4 (2.385 × 10− 1) | 1.487 × 10− 3 (9.999 × 10− 1) |
JUB | 1.486 × 10− 3 (9.507 × 10− 1) | 1.755 × 10− 3 (9.997 × 10− 1) | 2.445 × 10− 3 (1) | 3.674 × 10− 4 (2.385 × 10− 1) | 2.804 × 10− 3 (9.999 × 10− 1) |
MIA | 1.509 × 10− 3 (9.507 × 10− 1) | 4.210 × 10− 4 (6.298 × 10− 1) | 2.247 × 10− 3 (1) | 3.666 × 10− 4 (2.385 × 10− 1) | 2.432 × 10− 3 (9.999 × 10− 1) |
C4BPA | 2.241 × 10− 3 (9.999 × 10− 1) | 3.190 × 10− 4 (6.298 × 10− 1) | 1.307 × 10− 3 (1) | 6.000 × 10− 4 (2.951 × 10− 1) | 2.866 × 10− 3 (9.999 × 10− 1) |
CLDN6 | 2.653 × 10− 3 (9.999 × 10− 1) | 1.282 × 10−3 (9.997 × 10− 1) | 2.414 × 10− 3 (1) | 7.377 × 10− 4 (3.270 × 10− 1) | 1.542 × 10− 3 (9.999 × 10− 1) |
PALMD | 3.737 × 10− 3 (9.999 × 10− 1) | 1.151 × 10− 3 (9.997 × 10− 1) | 2.648 × 10−3 (1) | 1.127 × 10− 3 (3.776 × 10− 1) | 3.032 × 10− 3 (9.999 × 10− 1) |
KLK12 | 3.840 × 10− 3 (9.999 × 10− 1) | 2.766 × 10− 3 (9.997 × 10− 1) | 9.826 × 10− 4 (1) | 1.225 × 10− 3 (3.776 × 10− 1) | 3.162 × 10− 3 (9.999 × 10− 1) |