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"Functional Annotation Clustering" with default classification stringency is applied to derive all the related functions associating with their enrichment scores and P-values.
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After rinsing, the cartridge was placed in the NanoChip Reader where a specific thermal stringency was applied.
For statistical evaluation, different levels of stringency were applied so as to reflect stringency levels commonly found in the literature [8], [14], [16].
Two levels of stringency were applied.
Controls for false positives and significance stringency were applied accordingly based on each analysis.
The absence of PAD1 (Tb927.7.5930), recently identified as being up-regulated in stumpy forms at the mRNA and protein level [ 51], reflects the stringency of the threshold used, with this gene being detected, along with PAD 6 (Tb927.7.5980) and PAD8 (Tb927.7.6000) when the slightly reduced stringency was applied (adj P value < 0.1) (Additional file 4).
Two stringencies were applied: the standard FDR cut-off (≤10%) or the more stringent 'Benjamini' p-value (≤0.1).
Since this was a manageable list, and probably related to the direct effect of the treatment, no further stringency filters were applied thus removing experimenter involvement.
Different levels of stringency have been applied for the definition of CNEs [34], [40], mostly with the intention to select a manageable number of candidate elements rather than with a biologically based rationale.
Where ambiguous alignments were observed higher stringency filters were applied (sequence similarity higher than 97.5% and coverage higher than 90%).
Higher filter stringency can be applied by demanding a sequence variant to be present in two, three, or more isolates.
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