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We first simulate from a fixed effect size, conditional on significance of a two-sided Wald test at P< pcrit.
The information obtained here can be used to calculate the power (of testing feature for being DE) conditional on significance level α, for selected features.
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To address significance bias Zöllner and Pritchard [2007] proposed to maximize the likelihood of the genotype data conditional on it passing a significance threshold.
For the annotation of split nodes the "Path significance conditional on Split" enrichment p-value in the GUI was set to be ≤ 5·10−5.
These IBS regions are assessed for significance empirically, conditional on a model for LD and a genetic model (for recombination in the pedigree).
GISTIC assesses the significance of a 'new' region conditional on having found the previously most significant region(s) using a procedure the authors term the 'peel off' algorithm.
In a recent meta-analysis on smoking behavior, a novel SNP was identified with genome-wide significance related to smoking conditional on a known SNP [7].
A t test for each reported eQTL assessed significance of the interaction conditional on the v-eQTL, epistasis SNP and the eQTL.
To test the significance of each SNP conditional on the genotypes of other SNPs, logistic regression analysis was performed under the additive model for the minor allele.
Signal was then thresholded based on significance.
The corresponding P-value gives the significance of the anchor SNP conditional on the partner SNP.
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CEO of Professional Science Editing for Scientists @ prosciediting.com