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Notice the difference between the normalization curves at large A values.
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In dataset #3, the differences between the normalization approaches is less striking, illustrated by similarly shaped ROC curves and AUC values.
A potential cause of the observed difference between the tested normalization approaches is observed in the results on global level: the ranking of probes changes when using some normalization approaches, increasing the likelihood of un-enriched probes being spread over the whole dynamic range of the enriched probe distribution.
The results of known targets and enriched regions show consistent differences between the various normalization approaches.
Compared to the Golden Spike dataset (Fig. 8), the difference between normalization methods in the resulting degradation of the FDR was smaller for this dataset.
We can compare the AIC and ABIC values among the MLE based models and among the Bayesian models, respectively, although we cannot directly compare the AIC value with ABIC values here because we did not adjust the difference in the normalization factors between AIC and ABIC in the considered models.
The difference between normalization methods in terms of the resulting M values is substantial though less pronounced relative to the ALL dataset (Table 2).
As the contralateral leg was significantly stronger to start with, in the overall group and in the subgroups, which could affect fatigue difference between legs, a normalization of the fatigue results was done to the first contraction.
The only difference between these two normalization methods is the gene length, which is constant for a given gene across samples.
The reason for the difference between the genotypes could be the incomplete normalization of cbb1 plants.
After quantile normalization, the difference between the z-scores was calculated (Supplementary Table S1).
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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