Table 2 Minimum classification error rate estimated for each data set for the first best approaches (percentage) and the associated number of genes/SNPs that were selected.
Data set | rank 1 | rank 2 | rank 3 | rank 4 | rank 5 | rank 6 | rank 7 | rank 8 | rank 9 |
|---|---|---|---|---|---|---|---|---|---|
Leukemia | RFE | SPLSDA- LDA | LDA | SPLSDA- LOG | RF | DDA | sPLS | NSC | SGPLS |
error rate | 20.55 | 22.36 | 22.78 | 23.33 | 24.17 | 24.31 | 24.30 | 26.25 | 26.67 |
# genes | 5 | 200 | 7129 | 500 | 200 | 50 | 10 | 500 | 500 |
SRBCT | RF | OFW- cart | DDA | LDA | sPLS | NSC | SGPLS | RFE | SPLSDA- LDA |
error rate | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.63 | 1.27 | 1.58 | 1.90 |
# genes | 30 | 50 | 30 | 100 | 100 | 500 | 50 | 5 | 200 |
Brain | RFE | DDA | LDA | sPLS | RF | SPLSDA- LDA | NSC | OFW- cart | SPLSDA- LOG |
error rate | 10.56 | 10.78 | 11.11 | 11.22 | 11.89 | 14.45 | 15.11 | 15.56 | 17.00 |
# genes | 10 | 25 | 30 | 6144 | 500 | 35 | 20 | 35 | 50 |
GCM | RFE | LDA | RF | SGPLS- LDA | sPLS | OFW- svm | SGPLS- LOG | OFW- cart | NSC |
error rate | 0.81 | 1.14 | 1.22 | 1.63 | 3.41 | 4.01 | 4.71 | 4.88 | 7.23 |
# genes | 5 | 500 | 500 | 200 | 200 | 500 | 500 | 7129 | 10 |
SNP | NSC | DDA | SPLS | RFE | SPLSDA- LDA | RF | SPLSDA- LOG | OFW- cart | OFW- svm |
error rate | 6.50 | 11.54 | 11.71 | 12.36 | 13.01 | 17.40 | 31.22 | 49.96 | 51.67 |
# SNPs | 5000 | 1000 | 2000 | 20000 | 2000 | 20000 | 200 | 20000 | 20000 |