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Table 1 Estimation of true positive and false positive rates under varying significance thresholds using 1X to 5X samples and 90 normal test samples.

From: CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

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
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
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
  1. Notes:
  2. 1 SP: Single point analysis
  3. 2 KS: Kernel smoothing with 100 kb window after single point analysis
  4. 3 TR: Tree partitioning of the genome on the kernel smoothed result.
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