Table 3

True positives and false positives

Category

All probesets

Bound probesets

Total

Empty

102

59

10,104

FC = 1

12

63

2,495

Mixed, FC = 1

1

9

58

Mixed, FC > 1

43

50

69

FC = 1.2

1

9

168

FC = 1.5

123

150

169

FC = 1.7

144

167

179

FC = 2

125

134

139

FC = 2.5

161

166

176

FC = 3

89

90

92

FC = 3.5

166

170

186

FC = 4

167

173

175

TP detected

1,019

1,109

1,353

FP detected

114

124

12,657

The number of TPs and FPs at a true q-value of 0.10 for the alchemy method when all probesets are used and when only a subset of probesets with detected transcripts (bound - low, medium and high intensity probesets) are used.

Schuster et al. Genome Biology 2007 8:R126   doi:10.1186/gb-2007-8-6-r126