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Figure 4 | Genome Biology

Figure 4

From: A reanalysis of a published Affymetrix GeneChip control dataset

Figure 4

A plot of the true versus estimated q-values from simulations described in the text. The solid gray line shows the results averaged over 30 simulations when using a design similar to that of Choe et al. [1]. The solid black line is the analogous comparison when using three independent individuals. The dashed line represents equality; conservatively estimated q values should fall beneath this line. The Choe et al. [1] design produces anti-conservative q-values estimates due to the incorrect underlying p-values, while the more statistically sound design produces conservative q-value estimates. The Monte Carlo variation of the q-value estimates is small enough that these conclusions are not affected.

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