In addition, the examination of exactly the same dataset (and hence the same aspect of OSM) increases the reproducibility of the analyses, which becomes of particular interest if analyses are conducted at different points in time.
Of note, our analysis of the relationship between migration and HIV prevalence in sub-Saharan Africa used exactly the same dataset as the study noted above which found a positive association between female in-migration and HIV prevalence [ 24].
We prepared exactly the same five datasets as those used in ML analyses.
To assess BDS's scalability, we ran exactly the same pipeline on two datasets that vary in size by several orders of magnitude (Table 2): (i) a relatively small dataset (chromosome 20 subset, ∼2 GB) that would typically be used for development, testing and debugging and (ii) a high-depth whole-genome sequencing dataset (over 200× coverage, roughly 1.5 TB).
In such a situation, which is more typical than the earlier illustration example, one can use exactly the same method, applied to multiple datasets with different dynamic profiles, as long as one can validly assume that the functional forms are not affected by differences among the datasets.
Indeed, we re-estimated the underlying known parameters for each of these 100 "pseudo-empirical" datasets with exactly the same approach used for the ABC estimation performed with the empirical dataset (i. e. the 106 simulations of the best-fit model).
The outlying sample detected in the NMR dataset was exactly the same as in the cytokine/chemokine model.
This was then used to perform exactly the same analysis as described for our dataset.
Specifically, we first performed quantile normalization [ 68] for all expression profiles, so that each sample in the dataset achieved exactly the same distribution.
We constructed RF models on the TR299 dataset using exactly the same scheme as the original RF models and applied the models to predict putative DNA-binding residues in the test dataset TS75 whose SS information was predicted by the PREDATOR program (Frishman and Argos, 1997).
