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Our model-based approach also provides an intuitive P value based significance threshold for finding patch boundaries.
The difference among previously published studies and ours may be due to a more conservative permutation based significance cutoff in our Rqtl analysis.
PRESTO: The permutation based significance threshold from PRESTO was 7.6 × 10-8 (see Table 1).
It also provides Poisson likelihood based significance tests for edge counts (either pairs of genes and or pairs of diseases) that respect the underlying cluster structure.
20 We used Epicure software for parameter estimation and tests, 24 and we based significance tests and 95% confidence intervals on likelihood profiles.
However, the obtained Xd-score (0.26, which matches with the regression fit based significance threshold), highlights functional associations reflecting the abundance of molecular interactions between the corresponding proteins for these gene sets and their shared network neighbourhood (instead of only their directly shared genes/proteins).
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We used an extension of Stouffer's method [ 33] to estimate the overall significance based on the significance of the individual tests.
Covariates for multivariate analysis were selected based on significance (p value<0.05) in univariate analysis and significant covariates in the literature.
In this article, a floating-point system based on significance arithmetic will be described.
Signal was then thresholded based on significance.
Findings were prioritized based on significance thresholds and consistency across different analyses, and accounted for multiple testing and prior knowledge.
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