Table 4

Genes were ranked with the statistical methods in terms of degree of differential expression, and the number of true and false positives among the top 500 was counted. Above are the number of true and false positives in the top 500 when the proportion unchanged equals 5% and the number of genes equals 10000.
Method
 False positive
 True positive
lognormal
samroc
 262
 238
t-test
 296
 204
Wilcoxon
 303
 197
Fold Change
 454
 46
MG
 247
 253
Bayes
 284
 216
SAM
 286
 214
normal
samroc
 302
 198
t-test
 307
 193
Wilcoxon
 303
 197
Fold Change
 392
 108
MG
 454
 46
Bayes
 345
 155
SAM
 304
 196

Broberg Genome Biology 2002 3:preprint0007.1   doi:10.1186/gb-2002-3-9-preprint0007