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However we were able to allow for this possibility without incurring a multiple testing penalty.
These approaches reduced the multiple testing penalty by lowering the fraction of the genome probed to 0.19% of the total, while increasing the likelihood of studying SNPs within relevant BAV genes and pathways.
A discovery phase with insufficient stringency will likely lower a study's ability to replicate both main effects and interaction effects as the multiple testing penalty at the replication phase is increased.
First, it can reduce the number of tests performed and hence the multiple testing penalty incurred.
Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty.
The Bonferroni correction widely applied to human GWA analyses imposes a substantial multiple testing penalty, effectively limiting the ability to detect loci with small effects to reduce the detection of spurious loci.
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Conversely, Big Data will require additional multiple testing penalties, need for replication, even if reproducibility of results may be an issue and interpretability too.
In addition, the approach helps to manage the multiple testing penalties across numerous categories.
However, some researchers, mindful of historical difficulties of interpreting complex genetic data (17), prefer to apply a cautious approach to secure robust (i.e. taking into account stage 2 multiple testing penalties) and independent (of GWAS discovery) replication data (3, 4).
The pathway-level analysis that we performed was designed in part to minimize the multiple hypothesis testing penalty (Califano et al. 2012).
Olfactory responses had generally low to moderate broad-sense heritabilities, which combined with the multiple-testing penalty incurred by testing millions of variants for 14 odorants limited our ability to identify individual variants associated with olfactory behavior.
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