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Table 2 Area under the ROC curve derived from different stages of the CARAT method.

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

Area under ROC Curve

1X

3X

4X

5X

Stage 1

0.6240

0.5188

0.6575

0.7863

Stage 2

0.6732

0.5384

0.6840

0.8128

Stage 3

0.9319

0.8987

0.9546

0.9877

Stage 4

0.9887

0.9759

0.9974

0.9995

Stage 5

0.9999

0.9999

1.0000

1.0000

  1. Note:
  2. 1The specificity is estimated using the 47 female samples that are a subset of the 90 normal test set samples and is restricted to the 1955 X chromosome SNPs. The sensitivity is estimated on 1955 X chromosome SNPs using DNA samples with 1X, 3X, 4X and 5X chromosomes.
  3. 2Stage 1: Single point analysis: no probe selection, no intensity adjustment on fragment length and GC content; no intensity adjustment on reference mean.
  4. 3Stage 2: Stage 1 plus probe selection.
  5. 4Stage 3: Stage 2 plus intensity adjustment on the fragment length and GC content and intensity adjustment on the reference mean.
  6. 5Stage 4: Stage 3 plus kernel smoothing with a 100 kb window.
  7. 6Stage 5: Stage 4 plus genome partitioning using the regression tree.
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BMC Bioinformatics

ISSN: 1471-2105

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