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This exploratory approach, however, is known to cause inflation of a type I error because it conducts multiple correlated testing [ 36- 38].
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P values were adjusted for multiple correlated tests (PACT).
We used global tests of main effects and treatment interactions, adjusting the P-values for multiple correlated tests.
As mentioned in Leek and Storey (2007), q-values can be misleading when applied to multiple correlated tests.
In order to maintain the family-wise Type 1 error at 0.05 over the multiple (correlated) tests, we set the critical alpha at a conservative 0.01.
To avoid the burden of multiple correlated tests, we used only genotyped markers and discarded the pseudomarkers used for single-locus interval mapping.
To account for the correlated tests from the determination of a genetic model for a given SNP and for the multiple correlated tests from the SNPs within each gene region, we performed a P-value adjustment for correlated tests.
Permutations can naturally account for the fact that some genes have very few rare alleles (and thus can never produce a significant burden test result) and that multiple correlated tests might have been undertaken (31).
Finally, our rankings and determination of interesting SNPs was based on an adjusted P-value obtained using a method that accounts for multiple correlated tests when first determining the genetic model and then across all SNPs within each candidate gene region.
In both SNP-SNP and gene-gene interaction assays, we chose to use a nominal level of P <0.01 as the cutoff to identify important SNP pairs or gene pairs because no suitable methodologies for adjusting for multiple correlated tests of massive SNP pairs (or gene pairs) were available, which may have led to false positives.
This will involve: conducting conditional tests to identify the causal genetic variant among multiple correlated signals; testing whether the effect of PTSD genetic risk variants is moderated by age of first trauma, trauma type, and trauma severity; and exploring gene-gene interactions using a novel gene-based statistical approach.
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