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## Figure 1.
ChipStat behavior using simulated biological/experimental + hybridization noise model.
The behavior of the ChipStat algorithm was evaluated (
p_{ps }= 0.05, 16 probe pairs per probe set) using a Monte Carlo model in which the ratio
of biological + experimental noise (E(b) + E(p)) to hybridization noise (E(h)) is
constant (see text for further details). Results are shown for E(h) = 0 (Exp noise
only; blue), E(h) = E(b) + E(p) (Hyb noise = Exp noise; red), E(h) = 2 × (E(b) + E(p))
(Hyb noise = 2 × Exp noise; green), and E(b) + E(p) = 0 (Hyb noise only; yellow).
The total number of probe sets simulated (11,820) was chosen to match the number of
probe sets containing 16 probe pairs per probe set on the Affymetrix MG_U74Av2 array.
The number of probe pairs increasing by chance is shown on the x axis, and the fraction of total probe sets simulated is shown on the y axis. This simulation was repeated 100×, and the average of these results is shown.
(a) Probability of the indicated number of probe pairs increasing. (b) Cumulative P value (equal to or greater than the indicated number of probe pairs changing).
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