MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis

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.

ISSN: 1474-760X