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The threshold hook and the horizontal line provide the true and the apparent (false) thresholds for good RNA quality in terms of the logged 3′/5′-intensity ratios, Δ3′/5′ < Δthreshold.
After collecting the 50 p-values, the true positive rate corresponding to a given false positive threshold was estimated as the proportion of simulations identifying the true positive gene using the false positive threshold.
This model was inferior to the full model, with an AUC of 0.60 and 42% true positive rate at the 30% false positive threshold ('Basic model' in Fig. 3).
At a 1% false positive threshold 1863 nonredundant proteins or protein groups were identified.
The data from the simulations were used to calculate the true positive rate based on a given false positive threshold.
Due to the fixed false discovery threshold centroid probe numbers differed between data sets.
We corrected for multiple testing with a false discovery threshold of P < 0.05.
A 90% sensitivity (10% false positive) threshold was used to assign tumors to high and low risk groups.
However, if we perform two independent STs with the 0.05 false positive threshold, the probability that at least one test will be a false positive is 10%.
When one ST is performed and a false positive threshold of 0.05 is selected, the probability of rejecting the null hypothesis when it is true would be 5%.
Using a false discovery threshold of 1%, we identified and quantified 587 putative SUMO1 substrates and 815 putative SUMO2 substrates in A549 cells.
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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