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We chose threshold values that were approximately 3 standard deviations (SD) above the HU of PMMA measurement and below the HU of water, respectively.
We chose threshold amino acid identities of 96.0%, 95.8%, and 94.5% for On, Or, and Og BESs, respectively, so that 5% of the homologous BESs of each species were discarded (Additional File 18).
Since the genome wide GC content for Arabidopsis thaliana is known to be around 36% [ 35], we chose threshold occurrence percentage of 25% for C/G and 40% for A/T for a particular position in all spacers of the same length (N).
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We chose thresholds based on empirical calculations of the probabilities of false and successful detection after allowing for multiple testing over physicians or practices.
Hence, to reconcile results, we first chose thresholds for GARP (raw output ranged as integers 0 10) and Maxent (raw output ranged as a real number 0 100) results.
Among the respondents who identified a threshold, 79 physicians (33.6%) and 314 laypeople (41.5%) chose thresholds under 10%.
We chose thresholds that were close to genome-wide levels of significance and previously documented EWAS FDR threshold (Patel et al., 2010).
The values will be filtered according to the chosen threshold of the error gain.
Posterior probability maps denote the probability that the connectivity value exceeds a chosen threshold, conditional upon the noisy observations.
To judge this information adequately, one has to be aware of the variability of activation pattern dependent on chosen threshold.
(b) Mean quality score of all sequences (Phred score) relative to a chosen threshold of 30, indicating a 99.9% chance that a base is called correctly.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com