The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity

Learning to Rank Academic Experts in the DBLP Dataset

Expert finding is an information retrieval task that is concerned with the search for the most knowledgeable people with respect to a specific topic, and the search is based on documents that describe people's activities. The task involves taking a user query as input and returning a list of people who are sorted by their level of expertise with respect to the user query. Despite recent interest in the area, the current state-of-the-art techniques lack in principled approaches for optimally combining different sources of evidence. This article proposes two frameworks for combining multiple estimators of expertise. These estimators are derived from textual contents, from graph-structure of the citation patterns for the community of experts, and from profile information about the experts. More specifically, this article explores the use of supervised learning to rank methods, as well as rank aggregation approaches, for combing all of the estimators of expertise. Several supervised learning algorithms, which are representative of the pointwise, pairwise and listwise approaches, were tested, and various state-of-the-art data fusion techniques were also explored for the rank aggregation framework. Experiments that were performed on a dataset of academic publications from the Computer Science domain attest the adequacy of the proposed approaches.Comment: Expert Systems, 2013. arXiv admin note: text overlap with arXiv:1302.041

The substantive and practical significance of citation impact differences between institutions: Guidelines for the analysis of percentiles using effect sizes and confidence intervals

In our chapter we address the statistical analysis of percentiles: How should the citation impact of institutions be compared? In educational and psychological testing, percentiles are already used widely as a standard to evaluate an individual's test scores - intelligence tests for example - by comparing them with the percentiles of a calibrated sample. Percentiles, or percentile rank classes, are also a very suitable method for bibliometrics to normalize citations of publications in terms of the subject category and the publication year and, unlike the mean-based indicators (the relative citation rates), percentiles are scarcely affected by skewed distributions of citations. The percentile of a certain publication provides information about the citation impact this publication has achieved in comparison to other similar publications in the same subject category and publication year. Analyses of percentiles, however, have not always been presented in the most effective and meaningful way. New APA guidelines (American Psychological Association, 2010) suggest a lesser emphasis on significance tests and a greater emphasis on the substantive and practical significance of findings. Drawing on work by Cumming (2012) we show how examinations of effect sizes (e.g. Cohen's d statistic) and confidence intervals can lead to a clear understanding of citation impact differences

Anchor selection strategies for DIF analysis: Review, assessment, and new approaches

Differential item functioning (DIF) indicates the violation of the invariance assumption for instance in models based on item response theory (IRT). For item-wise DIF analysis using IRT, a common metric for the item parameters of the groups that are to be compared (e.g. for the reference and the focal group) is necessary. In the Rasch model, therefore, the same linear restriction is imposed in both groups. Items in the restriction are termed the anchor items. Ideally, these items are DIF-free to avoid artificially augmented false alarm rates. However, the question how DIF-free anchor items are selected appropriately is still a major challenge. Furthermore, various authors point out the lack of new anchor selection strategies and the lack of a comprehensive study especially for dichotomous IRT models. This article reviews existing anchor selection strategies that do not require any knowledge prior to DIF analysis, offers a straightforward notation and proposes three new anchor selection strategies. An extensive simulation study is conducted to compare the performance of the anchor selection strategies. The results show that an appropriate anchor selection is crucial for suitable item-wise DIF analysis. The newly suggested anchor selection strategies outperform the existing strategies and can reliably locate a suitable anchor when the sample sizes are large enough