Table 1

Comparison between NN and SVM (LibSVM and SMO)

Dataset

NN

LibSVM

SMO

S1_NPH_CH2

318

158

174

S1_NPH_CH3

398

138

95

S1_PH_CH2

132

88

87

S1_PH_CH3

210

48

111

S2_NPH_CH2

72

37

50

S2_NPH_CH3

88

34

40

S2_PH_CH2

176

71

120

S2_PH_CH3

236

154

139

S3_NPH_CH2

72

-

-

S3_PH_CH2

487

231

413

S3_PH_CH3

338

147

295

The values indicate the number of PSMs that the learning method could retrieve when considering a 1% FDR. The NN values were significantly better. The dashes indicate that the algorithm could not find a set of hits with 1% FDR, i.e., there is no point in the ROC curve corresponding to such an error rate.

Cerqueira et al. BMC Genomics 2012 13(Suppl 5):S4   doi:10.1186/1471-2164-13-S5-S4