Samples misclassified by the 5-gene model using FLDA and/or SVM
Sample . | FLDA . | SVM . | PLS3 . |
|---|---|---|---|
| C010.1.Th1* | 0.02 ± 0.29† | 0.12 ± 0.04† | 0.007 |
| C021.2.Th1‡ | -1.40 ± 0.40 | -0.03 ± 0.07 | 0.009 |
| C019.4.UT‡ | -0.49 ± 0.27 | -0.02 ± 0.05 | 0.007 |
| C052.1.UT | 0.12 ± 0.16† | -0.10 ± 0.03 | 0.007 |
| C078.1.UT | 0.50 ± 0.15† | -0.15 ± 0.03 | 0.006 |
| C045.1.UT | 0.05 ± 0.15† | -0.22 ± 0.03 | 0.006 |
| S108.1.05 | 2.73 ± 0.56 | -0.04 ± 0.09† | 0.033 |
| S161.1.10* | -6.35 ± 0.40† | -0.56 ± 0.05† | 0.001 |
| S157.3.15 | 0.74 ± 0.14 | -0.12 ± 0.03† | 0.004 |
| S160.1.15* | -2.19 ± 0.33† | -0.25 ± 0.05† | 0.075§ |
| S137.1.27* | -1.77 ± 0.25† | -0.16 ± 0.03† | 0.001 |
| S142.1.30* | -1.55 ± 0.36† | -0.08 ± 0.08† | 0.700§ |
| S156.1.30* | -0.61 ± 0.21† | -0.12 ± 0.04† | 0.001 |
| S140.1.39 | 0.75 ± 0.17 | -0.04 ± 0.04† | 0.004 |
| S133.1.46* | -1.30 ± 0.21† | -0.15 ± 0.03† | 0.002 |
| S130.1.48 | -1.78 ± 0.30† | 0.10 ± 0.07 | 0.939§ |
| S159.1.70 | 0.28 ± 0.10 | -0.15 ± 0.03† | 0.035 |
| S132.1.84* | -2.31 ± 0.25† | -0.24 ± 0.03† | 0.001 |
| S218.1.87* | -0.66 ± 0.20† | -0.44 ± 0.07† | 0.218§ |
Sample . | FLDA . | SVM . | PLS3 . |
|---|---|---|---|
| C010.1.Th1* | 0.02 ± 0.29† | 0.12 ± 0.04† | 0.007 |
| C021.2.Th1‡ | -1.40 ± 0.40 | -0.03 ± 0.07 | 0.009 |
| C019.4.UT‡ | -0.49 ± 0.27 | -0.02 ± 0.05 | 0.007 |
| C052.1.UT | 0.12 ± 0.16† | -0.10 ± 0.03 | 0.007 |
| C078.1.UT | 0.50 ± 0.15† | -0.15 ± 0.03 | 0.006 |
| C045.1.UT | 0.05 ± 0.15† | -0.22 ± 0.03 | 0.006 |
| S108.1.05 | 2.73 ± 0.56 | -0.04 ± 0.09† | 0.033 |
| S161.1.10* | -6.35 ± 0.40† | -0.56 ± 0.05† | 0.001 |
| S157.3.15 | 0.74 ± 0.14 | -0.12 ± 0.03† | 0.004 |
| S160.1.15* | -2.19 ± 0.33† | -0.25 ± 0.05† | 0.075§ |
| S137.1.27* | -1.77 ± 0.25† | -0.16 ± 0.03† | 0.001 |
| S142.1.30* | -1.55 ± 0.36† | -0.08 ± 0.08† | 0.700§ |
| S156.1.30* | -0.61 ± 0.21† | -0.12 ± 0.04† | 0.001 |
| S140.1.39 | 0.75 ± 0.17 | -0.04 ± 0.04† | 0.004 |
| S133.1.46* | -1.30 ± 0.21† | -0.15 ± 0.03† | 0.002 |
| S130.1.48 | -1.78 ± 0.30† | 0.10 ± 0.07 | 0.939§ |
| S159.1.70 | 0.28 ± 0.10 | -0.15 ± 0.03† | 0.035 |
| S132.1.84* | -2.31 ± 0.25† | -0.24 ± 0.03† | 0.001 |
| S218.1.87* | -0.66 ± 0.20† | -0.44 ± 0.07† | 0.218§ |
Patient samples are sorted by their tumor burden. Columns LDA and SVM contain average scores obtained by these samples ± standard deviation over the approximately 100 times that these samples were tested during 1000 random resamplings. The column labeled PLS3 displays the expression level of PLS3 (in terms of its ratio to the housekeeping gene relative to that in the Stratagene reference RNA sample).
Samples that were misclassified by both methods.
Scores assigned these samples to incorrect class (positive average scores for controls and negative average scores for patients).
Two control samples, C021.2.Th1 and C019.4.UT, were marginally classified by SVM, even though the average score turned out to be negative, and were considered to be misclassified.
Misclassified patients with high levels of PLS3 (with z score more than 5, relative to controls). These high-PLS3 patients may deserve special treatment, because high levels of PLS3 alone are very unusual for healthy individuals.