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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.
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BMC Bioinformatics

ISSN: 1471-2105

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