A statistical framework for the design of microarray experiments and effective detection of differential gene expression

Motivation: Microarray experiments generate a high data volume. However, often due to financial or experimental considerations, e.g. lack of sample, there is little or no replication of the experiments or hybridizations. These factors combined with the intrinsic variability associated with the measurement of gene expression can result in an unsatisfactory detection rate of differential gene expression (DGE). Our motivation was to provide an easy to use measure of the success rate of DGE detection that could find routine use in the design of microarray experiments or in post-experiment assessment.

Developing critical social work in theory and in practice: child protection and communicative reason

This paper argues that a critical analysis of the ideologies that inform contemporary child care has been missing from the ‘re-focusing debate’. Such an analysis points up the necessity of reasserting a critical social work position in order to provide a basis for reconstructing practice and engaging with other social actors and their ideologies in an open and creative fashion compatible with Habermas’ aspiration of ‘communicative reason’.

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses.

Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one.

Robustness in scale-free networks: Comparing directed and undirected networks

In this paper, scale-free networks and their functional robustness with respect to structural perturbations of the network are studied. Two types of perturbations are distinguished: random perturbations and attacks. The robustness of directed and undirected scale-free networks is studied numerically for two different measures and the obtained results are compared. For random perturbations, the results indicate that the strength of the perturbation plays a crucial role. In general, directed scale-free networks are more robust than undirected scale-free networks.

Struggles against Injustice:: Contemporary Critical Theory and Political Violence

This article investigates a significant problem in contemporary critical theory, namely its failure to address effectively the possibility that a campaign of political violence may be a legitimate means of fighting grave injustice. Having offered a working definition of ‘political violence’, I argue that critical theory should be focused on experiences of injustice rather than on ideals of justice. I then explore the reasons as to why, save for some intriguing remarks on retrospective legitimation, Jürgen Habermas has not addressed this issue directly. While Axel Honneth's recognition theory may have greater potential here, the absence of explicit consideration of the matter by him leaves considerable work to do. I introduce five questions in the concluding section that provide a starting point in setting out an appropriately stringent, normative test for claims that support violent action against injustice.