Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery

Han, Henry

doi:10.1186/1471-2105-11-S1-S1

BMC Bioinformatics

Table 2 Comparisons of the seven algorithms

From: Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery

	Average Classifying rate (%)	Average Sensitivity (%)	Average Specificity (%)
Ovarian
npca-svm-linear	98.94 ± 00.65	98.35 ± 01.03	99.98 ± 00.24
npca-svm-rbf	99.79 ± 00.35	100.0 ± 00.00	99.42 ± 00.99
svm-linear	99.50 ± 00.83	100.0 ± 00.00	98.63 ± 02.21
pca-svm-linear	99.96 ± 00.26	99.98 ± 00.17	99.93 ± 00.51
nmf-svm-linear	97.41 ± 00.94	99.91 ± 00.31	92.92 ± 02.50
knn	96.53 ± 01.57	99.28 ± 01.34	91.67 ± 03.67
pca-lda	99.67 ± 00.87	99.93 ± 00.38	99.21 ± 02.00
ica-svm-linear	99.99 ± 00.08	99.99 ± 00.12	100.0 ± 00.00
Ovarian-qaqc
npca-svm-linear	98.70 ± 00.89	98.01 ± 01.94	99.27 ± 00.90
npca-svm-rbf	98.91 ± 00.98	98.11 ± 02.25	99.57 ± 00.82
svm-linear	96.57 ± 01.99	96.16 ± 03.52	96.97 ± 02.19
pca-svm-linear	97.12 ± 01.17	97.14 ± 02.16	97.94 ± 01.57
nmf-svm-linear	88.69 ± 03.47	92.02 ± 05.01	86.24 ± 05.67
knn	90.87 ± 02.92	89.99 ± 04.68	91.82 ± 04.43
pca-lda	97.69 ± 00.65	98.81 ± 01.68	96.99 ± 00.03
ica-svm-linear	97.56 ± 01.45	97.80 ± 02.46	97.41 ± 01.77
Liver
npca-svm-linear	96.02 ± 01.35	97.68 ± 01.71	94.40 ± 02.22
npca-svm-rbf	97.25 ± 01.30	98.35 ± 01.67	96.20 ± 02.01
svm-linear	91.78 ± 02.27	92.57 ± 03.84	91.04 ± 03.76
pca-svm-linear	90.21 ± 01.99	90.96 ± 03.69	89.57 ± 03.56
nmf-svm-linear	77.76 ± 02.48	84.58 ± 05.14	71.30 ± 05.12
knn	76.48 ± 02.20	72.27 ± 04.60	80.80 ± 04.57
pca-lda	90.08 ± 02.13	91.39 ± 03.53	88.87 ± 03.95
ica-svm-linear	86.61 ± 02.87	87.78 ± 04.55	86.50 ± 04.86
Colorectal
npca-svm-linear	98.14 ± 01.27	97.93 ± 02.32	98.35 ± 02.00
npca-svm-rbf	97.15 ± 01.07	95.81 ± 02.78	98.18 ± 02.22
svm-linear	96.55 ± 01.87	94.35 ± 03.47	98.26 ± 02.16
pca-svm-linear	93.21 ± 03.38	92.59 ± 04.68	93.89 ± 05.56
nmf-svm-linear	94.73 ± 03.09	92.71 ± 06.14	96.49 ± 03.45
knn	95.05 ± 03.17	96.17 ± 02.91	94.28 ± 05.33
pca-lda	94.05 ± 02.78	94.16 ± 03.74	94.01 ± 04.12
ica-svm-linear	96.04 ± 02.02	94.38 ± 03.66	97.39 ± 02.97

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