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De Neve J.,Statistics and Bioinformatics | Meys J.,Statistics and Bioinformatics | Ottoy J.-P.,Statistics and Bioinformatics | Clement L.,Ghent University | And 2 more authors.
Bioinformatics | Year: 2014

Motivation: Recently, De Neve et al. proposed a modification of the Wilcoxon-Mann-Whitney (WMW) test for assessing differential expression based on RT-qPCR data. Their test, referred to as the unified WMW (uWMW) test, incorporates a robust and intuitive normalization and quantifies the probability that the expression from one treatment group exceeds the expression from another treatment group. However, no software package for this test was available yet. Results: We have developed a Bioconductor package for analyzing RT-qPCR data with the uWMW test. The package also provides graphical tools for visualizing the effect sizes. © The Author 2014. Published by Oxford University Press. All rights reserved.

Graler B.,University of Munster | Van Den Berg M.J.,Ghent University | Vandenberghe S.,Ghent University | Petroselli A.,University of Tuscia | And 5 more authors.
Hydrology and Earth System Sciences | Year: 2013

Most of the hydrological and hydraulic studies refer to the notion of a return period to quantify design variables. When dealing with multiple design variables, the well-known univariate statistical analysis is no longer satisfactory, and several issues challenge the practitioner. How should one incorporate the dependence between variables? How should a multivariate return period be defined and applied in order to yield a proper design event? In this study an overview of the state of the art for estimating multivariate design events is given and the different approaches are compared. The construction of multivariate distribution functions is done through the use of copulas, given their practicality in multivariate frequency analyses and their ability to model numerous types of dependence structures in a flexible way. A synthetic case study is used to generate a large data set of simulated discharges that is used for illustrating the effect of different modelling choices on the design events. Based on different uni-and multivariate approaches, the design hydrograph characteristics of a 3-D phenomenon composed of annual maximum peak discharge, its volume, and duration are derived. These approaches are based on regression analysis, bivariate conditional distributions, bivariate joint distributions and Kendall distribution functions, highlighting theoretical and practical issues of multivariate frequency analysis. Also an ensemble-based approach is presented. For a given design return period, the approach chosen clearly affects the calculated design event, and much attention should be given to the choice of the approach used as this depends on the real-world problem at hand. © 2013 Author(s).

Rehman U.,Statistics and Bioinformatics | Vesvikar M.,Statistics and Bioinformatics | Maere T.,Statistics and Bioinformatics | Guo L.,Laval University | And 2 more authors.
Water Science and Technology | Year: 2015

Complete mixing is hard to achieve in large bioreactors in wastewater treatment plants. This often leads to a non-uniform distribution of components such as dissolved oxygen and, hence, the process rates depend on them. Furthermore, when these components are used as input for a controller, the location of the sensor can potentially affect the control action. In this contribution, the effect of sensor location and the choice of setpoint on the controller performance were examined for a non-homogeneously mixed pilot bioreactor described by a compartmental model. The impacts on effluent quality and aeration cost were evaluated. It was shown that a dissolved oxygen controller with a fixed setpoint performs differently as a function of the location of the sensor. When placed in a poorly mixed location, the controller increases the aeration intensity to its maximum capacity leading to higher aeration costs. When placed just above the aerated zone, the controller decreases the aeration rate resulting in lower dissolved oxygen concentrations in the remainder of the system, compromising effluent quality. In addition to the location of the sensor, the selection of an appropriate setpoint also impacts controller behavior. This suggests that mixing behavior of bioreactors should be better quantified for proper sensor location and controller design. © IWA Publishing 2015.

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