Table 1

Comparing the results of RAMA to the averaged log ratios on the HIV data and the like and like data

Data

Benchmark

RAMA

Averaged log ratio

HIV data

13 positive controls

All 13 positive controls have log ratios >1

All 13 positive controls have log ratios >1

24 negative controls

All 24 negative controls have log ratios <1

3 negative controls have log ratios >1

Like and like data

No genes expected to be differentially expressed

All log ratios <1

6 genes with log ratios >1

RAMA produced the desired results on both datasets while the averaged log ratio produced three and six false positives, respectively, on these two datasets.

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