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Decreasing the stringency of the homology cut-off allows us to obtain partial homology.
In contrast, decreasing the stringency of Param4 resulted in a decrease in the number of detected clusters (Fig. 3c).
Increasing the number of probes to 25 by decreasing the stringency of the T test (p = 0.15) resulted in a less robust predictor (13 cancers incorrectly assigned, 85.4%).
The number of clusters increased by decreasing the stringency of Param1 and Param2 simply because of the increased sensitivity for seed detection.
These data suggest that decreasing the stringency of the search (increasing the intervening arbitrary residue number) impairs the fidelity of the search.
Decreasing the stringency of the threshold initially improved performance, but at thresholds of less than 0.001, the difference became less significant, summarized by the plot of mean average precision (see Additional file 4).
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For smaller scaffolds, it was necessary to decrease the stringency of selection parameters to obtain SNP calls.
The results were largely robust to variation in this threshold, with the primary effect being that decreasing the stringency increased both the FDR and the number of hits.
Further increase of CNV calling stringency resulted in reduced sensitivity, while further decreasing the calling stringency produced excessive private CNV calls with noninteger segment means, suggestive of false positives.
The majority of in silico detected SNPs (55.4 %) were detected at PSNP ≥ 0.99, and most of the remaining SNPs were detected by decreasing the detection stringency to 0.80.
The number of tag types differentially expressed decreased by 57% as the stringency of the p-value increased from p ≤ 0.05 to 0.001.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com