Table 2

Comparing the results of BRIDGE to t-test and SAM on the HIV data and the Affymetrix spike-in data

t-test

Dataset

Benchmark

BRIDGE

p-value cut-off 0.01, no correction

p-value cut-off 0.05, standard Bonferroni correction

SAM

HIV data

13 positive controls, 24 negative controls

DE

13

14

1

12

TP

13

13

1

12

FP

0

1

0

0

Affymetrix spike-in data

65 spike-in genes

DE

45

33

4

8

TP

45

31

4

8

FP

0

2

0

0

For each dataset and each method, the number of differentially expressed (DE) genes, true positives (TP) and false positives (FP) are shown. For each dataset, the maximum TP and the minimum FP across all methods are shown in bold. BRIDGE produced the best results on both datasets in identifying the highest number of true positives without any false positives.

Chu et al. Genome Biology 2008 9:R118   doi:10.1186/gb-2008-9-7-r118