Table 2

ANOVA analysis for prediction performance (AUC)
gene selection method no. significant wins network based
PAM 4 No
sigGenNB 3 No
sigGenSVM 2 No
SCAD 6 No
HHSVM 9 No
RFE 1 No
RRFE 6 Yes
graphK 2 Yes
graphkKp 1 Yes
networkSVM 1 Yes
PAC 0 Yes
aveExpPath 9 Yes
HubClassify 6 Yes
pathBoost 4 Yes
network based (average) 3.625
classical (average) 4.17

PAM (prediction analysis of microarray data), sigGenNB (SAM + Naïve Bayes), sigGenSVM (SAM + SVM),SCAD-SVM, HHSVM (Huberized Hinge loss SVM), RFE (Recursive Feature Elimination), RRFE (Reweighted Recursive Feature Elimination), graphK (graph diffusion kernels for SVMs), graphKp (p-step random walk graph kernel for SVMs), networkSVM (Network-based SVM), PAC (Pathway Activity Classification), aveExpPath (average pathway expression), HubClassify (classification by significant hub genes), pathBoost.

Cun and Fröhlich

Cun and Fröhlich BMC Bioinformatics 2012 13:69   doi:10.1186/1471-2105-13-69

Open Data