Table 2.

Significant genes identified by the 3 methods (SAM, SVA, and LRA) using FDR equal to 10% and fold change greater than 1.25

 Methods
Method 1: SAMMethod 2: SVAMethod 3: LRA
Upregulated genes
 Significant genesDP174918591773
VP463370428
 Intersection288228274
 ConsistencyaDP VP1314 (75%) 446 (96%)1366 (73%) 351 (95%)1344 (76%) 411 (96%)
Downregulated genes
 Significant genesDP106110581030
VP246288243
 Intersection302631
 ConsistencyaDP VP847 (80%) 152 (62%)844 (80%) 146 (51%)837 (81%) 154 (63%)
Overall
 Significant genesDP281029172803
VP709658671
 Intersection318254305
 ConsistencyaDP VP2158 (77%) 597 (85%)2210 (76%) 497 (76%)2181 (78%) 565 (84%)
  • aConsistency is defined as the proportion of significantly upregulated (or downregulated) genes in the DP (VP) phase that are also upregulated (or downregulated) in the VP (DP) phase.