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A lean core region with a narrow probability density distribution and a small standard deviation of the solids concentration exists, while the wall region exhibits a high solids concentration with a wide probability density distribution and a large standard deviation of the solids concentration.
The latter observation can be explained as the predictions are done with a single, genome wide probability.
Given 0.05 as the desired experiment wide probability of type I error, a significance cutoff within about an order of magnitude of 10-5 was estimated.
The p-value assigned to each cluster depends on the success probability, and in G+C rich chromosomes the genome wide probability is much lower than the chromosome probability.
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The software calculates a likelihood ratio statistic (LRS) for each combination of marker and probeset, and uses permutation to estimate an empirical genome-wide probability of obtaining such a score, accounting for multiple testing [5].
The mean change in species' mean state-wide probability of occurrence was also greater for Maxent-based predictions than for GAM-based predictions, as was the number of species whose distributions were predicted to decrease.
Permutation test (1,000 replications) was used to determine the significance level for LOD with a genome-wide probability of P < 0.05.
The genome-wide probability was further derived from the chromosome-wide probability using an approximate Bonferroni correction: (1) Pgenome − wide = 1 − 1 − Pchromosome − wide 1 / r in which r was obtained by dividing the length of a specific chromosome by the length of the genome considered for QTL detection (3,3918 cM), as in [ 2].
By doing so, we create a genome-wide probability that a copy-number variation with a particular size independent of its genomic location will be detected by a microarray platform.
Moreover, we computed genome-wide probabilities of reporting differential gene activities for the Pre, TvN, and Meta stages, respectively.
To analyze these data further, we calculated the unconditional genome-wide probabilities of perfect colocalization, which are the most conservative and rigorous criteria possible.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com