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However, selection of the correct threshold plays a crucial role in deciding the SNR value.
However, the determination of the correct threshold is usually a critical issue as it usually depends on the genome under consideration.
The benefit of the correct threshold model increases as the proportion of the censored observations increase.
Even though our results do not confirm the practical superiority of the correct threshold model over the linear Gaussian model, we urge caution when applying a Gaussian model directly for an ordinal data.
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The formulae can be easily used to provide the correct threshold of type 1 error rate and to calculate the power when designing experiments or data collection protocols.
If one performs the standard Bonferroni correction (Bonferroni, 1936), which divides the significance threshold α (typically 0.05 or 0.01) by the number of tests, then the corrected threshold will be so low that hardly any finding will be statistically significant.
Specifically, it is useful to consider the midpoint of the psychometric function, the 75% correct threshold.
However, practical applications of POT method are confounded by the indeterminate nature of correct threshold beyond which the Pareto model becomes effective.
There was also a cluster of SNPs on the distal portion of chromosome 13 that showed a suggestive association with skin color, but all fell short of the corrected significance threshold.
A position is considered a putative variant if the P-value for both directions of one pool-pair reaches below the Bonferroni corrected threshold of α=0.05/(2× I), where I is the number of sequence positions.
Fourthly, a threshold false positive rate (p-value) of 0.01 was adopted as a threshold to validate the associations, instead of using a corrected threshold (e.g. the Bonferroni correction), or one for the false discovery rate.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com