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Such threshold value is deemed to be a stringent value for exclusion of descriptors displaying mild intercorrelation with one another whereas a high threshold value of 0.9, for instance, would allow fewer removal of descriptors while allowing descriptor pairs with mild intercorrelation to be included in the model.
To reduce the number of false predictions, the maximum expectation threshold was set to a stringent value of 2.0.
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Hence, to determine the sensitivity of ABS-Scan, a cut-off of 0.5, which is a more stringent value, is chosen.
ISL was statistically significant at a less stringent value (p<0.05) for Al stress.
In total, 339 predictions showed a more stringent value of p ≥ 0.9.
The recommended inflation value (1.5) plus a very stringent value (5) was selected to study the robustness of the detection.
Using a more stringent value of D' = 0.9 results in 2,906 more "independent" SNPs on chromosome 1 which extrapolates to 63,932 more "independent" SNPs across the genome.
The only exception is when using a highly stringent value, C = 0.1, for which the percentage of true positives reaches ~80% and the sensitivity ~20%.
The maximum expected value for BLAST (BLAST E) was changed from the default setting of 5e-3 to a more stringent value of 5e-15 in order to eliminate the possibility of false positives.
Considering that databases at Genbank are larger than our ad hoc databases, we adjusted the E threshold to a less stringent value (~1 to 6E-4), maintaining S' constant (~50) and following the equation E = mn2-S' [ 53].
Decreasing the threshold to a less stringent value such as 15 ("very strong evidence" according to Jeffreys' rule) reduced substantially the FNR (FNR<31% when α i <-4 and FNR<51% when α i <-2) and increased only slightly the FDR.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com