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Step 2: Decide the precision level c.
Our results allowed us to estimate the precision level of laboratory subproteome studies and we show here that, on average, recent high-precision computational methods such as PSORTb now have a lower error rate than laboratory methods.
However, using the maximum value could inflate the variance and lower the precision of our estimates.
The higher the sensitivity, the lower the precision [ 5].
Just as in yeast, its categorical edge classification reduces the correctness of the ranking of its clusters, giving lower precision levels.
At match_thresh = 0.5, STR achieves almost the same recall as SWC with only slightly lower precision levels, but its recall and precision are much worse at a higher match_thresh = 0.75.
However, since the penalty cost for false negatives is not high, the acceptable precision level can be lower.
BOOST achieves similar recall as STR but with substantially lower precision levels at both match thresholds.
As SSS' predictions are limited to small complexes, which is moreover a difficult challenge with a perfect matching requirement, it has lower precision levels compared to PPI+COMBINE.
Since it classifies edges categorically, many edges have similar scores that do not vary with classification accuracy; thus the ranking of clusters (based on their weighted-densities) does not correlate as well with their correctness, giving lower precision levels.
Such entities contribute to lowering the precision.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com