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It should be noted, that though each score is represented in a separate image for simplicity in viewing, the best criteria for an active compound is that BOTH the DS and eM scoring thresholds be met (DS ≤ −7 kcal/mol and eM ≤ −50 kcal/mol, respectively) [69 71].
Phosphorylated and unphosphorylated peptide sequences were identified if they initially passed the following Sequest scoring thresholds against the target database: 1+ ions, Xcorr ≥2.0 Sf ≥0.4, P≥5; 2+ ions, Xcorr ≥2.0, Sf ≥0.4, P≥5; 3+ ions, Xcorr ≥2.60, Sf ≥0.4, P≥5 against the target protein database.
To further explore the scoring thresholds that predict progression, a logistic regression was performed on the continuous immunohistochemistry scores.
Table 8 and Table 9 report results of GO-based annotation for respectively CFinder and MCODE modules whose values have not passed our confidence scoring thresholds.
Reference conditions and metric scoring thresholds were developed using a combination of historical records, best available data, and expert judgement.
Therefore, the use of any empirical scoring thresholds needs to be constantly reevaluated as new experimental data emerges.
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Logarithm of odds (LOD) score thresholds ≥ 7 was used to group the markers.
To group all 1,814 markers, logarithm of odds (LOD) score thresholds ≥ 7 were used.
These results are dependent on the choice of the scoring threshold (see Table 2 and 3).
A scoring threshold of 500 rfu in fluorescence intensity was set up to detect peaks.
Furthermore, the scoring threshold is also an important source for deviating results between studies.
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