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Chunk #12 — MATERIALS AND METHODS — False Discovery Rate Analysis

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Nicotine withdrawal sensitivity, linkage to chr6q26, and association of OPRM1 SNPs in the SMOking in FAMilies (SMOFAM) sample.
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To assign false discovery probabilities to individual OPRM1 SNPs included in the FBAT, false discovery rate (FDR) Q-values were calculated (40). Briefly, while P-values express the probability of a single false-positive result among all tests, Q-values estimate the proportion of results declared interesting that are actually false (41). As suggested by Storey et al (42) for analyses with few numbers of P-values, the bootstrap option was utilized in preference to the smoother option in generation of the Q-values. The authors suggest that the bootstrap method provides more reliable estimates under these conditions (42). We opted to not employ a specific Q-value threshold but rather present the Q-values in relationship to P-values and biological plausibility.