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Table 1 Validation of BABAR by comparison with limma normalisation for the detection of differentially-expressed genes

From: BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets

  Number of down-regulated genes detected
Virulence genes BABAR unique Both methods limma unique
SPI1 (40) 1 28 1
SPI2 (31) 4 10 2
SPI4 (6) 1 4 1
SPI5 (11) 1 3 0
Other genes    
Chemotaxis (9) 1 5 0
Flagellae (23) 2 4 1
  1. The number of down-regulated genes detected by the QGEE software (p ≤ 0.01) for the IHF dataset [22] (WT versus ihfAB double mutant) following either BABAR or limma quantile normalisation. The number of genes in each group is given in brackets (120 in total). Chemotaxis genes include che and mot genes; flagellae genes include flg, fli and flj genes.