Increasing digitalization in animal farming, commonly addressed as Precision Livestock Farming (PLF), offers benefits in terms of productivity, sustainability, reduced labor and improved monitoring of animal welfare. However, the large amounts of collected data must be stored, processed and evaluated in a proper way. In practice, challenges of continuous and exact data collection can arise, e.g., from air pollutants like dust occluding cameras and sensors, degrading material, the ever-present commotion caused by animals, workers and machines, regularly required maintenance or weak signal transmission. In this study, we analyzed the quality of multi-source spatio-temporal data from a broiler house with 8100 birds over a period of 31 months collected by the Farmer Assistant System (FAS). This is a ceiling-suspended robot equipped with several sensors and cameras that continuously collect data while moving through the barn. The data analysis revealed numerous irregularities: missing values, outliers, repetitive measurements, systematic errors, and temporal and spatial inconsistencies. About 40–50% of all records collected with the early version of the FAS had to be sorted out. The newer version of FAS provided cleaner data, although still about 10–20% of the data had to be removed. Our study has shown that where sophisticated technological systems meet a challenging environment, a thorough and critical review of data completeness and quality is crucial to avoid misinterpretation. The pipeline developed here is designed to help developers and farmers detect failures in signal processing and localize the problem in the hardware components. Scientists, industrial developers and farmers should work more closely together to develop new PLF technologies to more easily advance digitization in agriculture.

Background: Unsupervised clustering and outlier detection are important in medical research to understand the distributional composition of a collective of patients. A number of clustering methods exist, also for high-dimensional data after dimension reduction. Clustering and outlier detection may, however, become less robust or contradictory if multiple high-dimensional data sets per patient exist. Such a scenario is given when the focus is on 3-D data of multiple organs per patient, and a high-dimensional feature matrix per organ is extracted.Methods: We use principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE) and multiple co-inertia analysis (MCIA) combined with bagplots to study the distribution of multi-organ 3-D data taken by computed tomography scans. After point-set registration of multiple organs from two public data sets, multiple hundred shape features are extracted per organ. While PCA andt-SNE can only be applied to each organ individually, MCIA can project the data of all organs into the same low-dimensional space.Results: MCIA is the only approach, here, with which data of all organs can be projected into the same low-dimensional space. We studied how frequently (i.e., by how many organs) a patient was classified to belong to the inner or outer 50% of the population, or as an outlier. Outliers could only be detected with MCIA and PCA. MCIA andt-SNE were more robust in judging the distributional location of a patient in contrast to PCA.Conclusions: MCIA is more appropriate and robust in judging the distributional location of a patient in the case of multiple high-dimensional data sets per patient. It is still recommendable to apply PCA ort-SNE in parallel to MCIA to study the location of individual organs.

The emerging zoonotic West Nile virus (WNV) has serious impact on public health. Thus, understanding the molecular basis of WNV infections in mammalian hosts is important to develop improved diagnostic and treatment strategies. In this context, the role of microRNAs (miRNAs) has been analyzed by several studies under different conditions and with different outcomes. A systematic comparison is therefore necessary. Furthermore, additional information from mRNA target expression data has rarely been taken into account to understand miRNA expression profiles under WNV infections. We conducted a meta-analysis of publicly available miRNA expression data from multiple independent studies, and analyzed them in a harmonized way to increase comparability. In addition, we used gene-set tests on mRNA target expression data to further gain evidence about differentially expressed miRNAs. For this purpose, we also studied the use of target information from different databases. We detected a substantial number of miRNA that emerged as differentially expressed from several miRNA datasets, and from the mRNA target data analysis as well. When using mRNA target data, we found that the targetscan databases provided the most useful information. We demonstrated improved miRNA detection through research synthesis of multiple independent miRNA datasets coupled with mRNA target set testing, leading to the discovery of multiple miRNAs which should be taken into account for further research on the molecular mechanism of WNV infections.

Outliers in the training or test set used to fit and evaluate a classifier on transcriptomics data can considerably change the estimated performance of the model. Hence, an either too weak or a too optimistic accuracy is then reported and the estimated model performance cannot be reproduced on independent data. It is then also doubtful whether a classifier qualifies for clinical usage. We estimate classifier performances in simulated gene expression data with artificial outliers and in two real-world datasets. As a new approach, we use two outlier detection methods within a bootstrap procedure to estimate the outlier probability for each sample and evaluate classifiers before and after outlier removal by means of cross-validation. We found that the removal of outliers changed the classification performance notably. For the most part, removing outliers improved the classification results. Taking into account the fact that there are various, sometimes unclear reasons for a sample to be an outlier, we strongly advocate to always report the performance of a transcriptomics classifier with and without outliers in training and test data. This provides a more diverse picture of a classifier’s performance and prevents reporting models that later turn out to be not applicable for clinical diagnoses.