|
Estimation of true positive and false positive rates under varying significance thresholds using 1X to 5X samples and 90 normal test samples. |
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| Sample and Data |
Stage |
p-value < 10-2 |
p-value < 10-4 |
p-value < 10-6 |
Total |
|||
|
|
||||||||
| Count |
Percent |
Count |
Percent |
Count |
Percent |
Count |
||
|
|
||||||||
| 90 normal samples (autosomes) |
SP |
409049 |
5.05% |
42182 |
0.52% |
11154 |
0.14% |
8095770 |
| KS |
40247 |
0.497% |
3302 |
0.041% |
770 |
0.009% |
8095770 |
|
| TR |
5417 |
0.067% |
506 |
0.006% |
167 |
0.002% |
8095770 |
|
| 1X |
SP |
1441 |
73.71% |
694 |
35.50% |
286 |
14.63% |
1955 |
| KS |
1780 |
91.05% |
714 |
36.52% |
111 |
5.68% |
1955 |
|
| TR |
p-value = 1.99 × 10-4 |
1955 |
||||||
| 3X |
SP |
1271 |
65.01% |
879 |
44.96% |
603 |
30.84% |
1955 |
| KS |
1707 |
87.31% |
1136 |
58.11% |
547 |
27.98% |
1955 |
|
| TR |
p-value = 8.13 × 10-6 |
1955 |
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| 4X |
SP |
1726 |
88.29% |
1523 |
77.90% |
1343 |
68.70% |
1955 |
| KS |
1929 |
98.67% |
1861 |
95.19% |
1697 |
86.80% |
1955 |
|
| TR |
p-value = 6.15 × 10-12 |
1955 |
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| 5X |
SP |
1884 |
96.37% |
1801 |
92.12% |
1724 |
88.18% |
1955 |
| KS |
1950 |
99.74% |
1933 |
98.87% |
1907 |
97.54% |
1955 |
|
| TR |
p-value = 1.50 × 10-16 |
1955 |
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|
Notes: 1 SP: Single point analysis 2 KS: Kernel smoothing with 100 kb window after single point analysis 3 TR: Tree partitioning of the genome on the kernel smoothed result. | ||||||||
Huang et al. BMC Bioinformatics 2006 7:83 doi:10.1186/1471-2105-7-83 |
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