Table 5.

Binomial probabilities, with 95% confidence intervals in parentheses, for TPs detected using alternative analysis, corresponding to three different coverage values

Platform	Coverage
	Alternative analysis for amplifications			Alternative analysis for deletions
	0.1 Mb (lower, upper)	0.5 Mb (lower, upper)	1 Mb (lower, upper)	0.1 Mb (lower, upper)	0.5 Mb (lower, upper)	1 Mb (lower, upper)
Affymetrix 6.0	0.36 (0.24, 0.49)	0.69 (0.56, 0.8)	0.77 (0.64, 0.86)	0.04 (0, 0.21)	1 (0.86, 1)	1 (0.86, 1)
Affymetrix 2.7M	0.25 (0.15, 0.37)	0.44 (0.31, 0.57)	0.45 (0.33, 0.58)	0.54 (0.33, 0.74)	0.96 (0.79, 1)	0.96 (0.79, 1)
Agilent 1M	0.38 (0.26, 0.5)	0.7 (0.58, 0.81)	0.73 (0.61, 0.84)	0.83 (0.63, 0.95)	0.88 (0.68, 0.97)	0.92 (0.73, 0.99)
Illumina 1M Duo	0.44 (0.31, 0.57)	0.7 (0.58, 0.81)	0.75 (0.63, 0.85)	0.21 (0.07, 0.42)	0.92 (0.73, 0.99)	0.96 (0.79, 1)
NimbleGen 2.1M	0.34 (0.23, 0.47)	0.73 (0.61, 0.84)	0.81 (0.7, 0.9)	0.92 (0.73, 0.99)	1 (0.86, 1)	1 (0.86, 1)
NimbleGen 3x720K	0.34 (0.23, 0.47)	0.75 (0.63, 0.85)	0.8 (0.68, 0.89)	1 (0.86, 1)	1 (0.86, 1)	1 (0.86, 1)

Data graphed in Figure 5c and d.