Motivation: The continued progress in developing technological platforms, availability of many published experimental datasets, as well as different statistical methods to analyze those data have allowed approaching the same research question using various methods simultaneously.
This behaviour of PBC may be desirable with many datasets, such as several independent lineages of parasites on the same host lineage, as in the original BPA approach to infer the host from associate cladograms [ 37].
One particular approach consists in gathering as many datasets from the literature as possible, pool them together and treat them as just one large data set, an approach that has given positive and encouraging results [ 8, 10, 11] In a previous work we applied this technique to two phylogenetically widely different bacteria, E. coli and B. subtilis [ 12].
We argue that, so far in this broad area of research, as many datasets have been used as research papers written, thus preventing confident reasoning about the relative performance of different techniques used in different publications.
In addition, with rapid accumulation of data in public repositories, new challenges arise from the urgent need to effectively integrate many different RNA-seq datasets, as well as different levels omics data to study the biological complexity and ultimately facilitate the precision and personalized medicine.
Empirical results obtained through application of the SampleNetwork R function to many datasets indicated that as outlying samples are removed, data are normalized, and technical artifacts (e.g. batch effects) are corrected, Z. K and Z. C exhibit a progressively linear, inverse relationship.
As in many datasets, even computation of an 50000×50000 correlation matrix using the built-in function cor becomes troublesome (R reports an error due to lack of memory).
Computer simulation study A computationally intensive study that creates many datasets with known characteristics (such as the true treatment effect in a randomised controlled trial) to investigate and illustrate statistical properties (such as bias) of an analytical approach.
As a result, many datasets are not public, and those that are publicly available are of limited size.
The Austrian Marchfeld region has been chosen as case study analysis because many datasets (Table 1) are readily available.
