1,721,007 research outputs found
Bayesian clustering of gene expression microarray data for subgroup identification.
No full textLa tecnologia per la raccolta di dati genetici si sta sviluppando con grande
rapidit`a generando grandi basi di dati, con particolare riferimento alle osservazioni microarray
riferite all’ “espressione ” di geni. Sorge quindi l’esigenza di sviluppare analisi
statistiche capaci di raccogliere questa sfida, anche se finora queste rimangono spesso confinate
in un ambito descrittivo. Recentemente tuttavia sono stati proposti modelli ispirati
all’impostazione bayesiana che hanno il pregio di fornire una base probabilistica coerente
alle categorie concettuali impiegate (quali raggruppamento, profilo molecolare etc), oltre
a consentire stime pi`u efficienti, grazie al cosiddetto effetto di borrowing strength. In
particolare sono stati proposti modelli gerarchici bayesiani nei quali le osservazioni sono
generate da una distribuzione mistura a tre componenti (a seconda che il gene sia sottoespresso,
normalmente espresso e sovraespresso); le distribuzioni iniziali dei parametri
sono invece basate sull’ipotesi tradizionale di scambiabilit`a. In questo lavoro proponiamo
un modello gerarchico nel quale i parametri che rappresentano le probabilit`a che i
geni provengano dalla componente sotto- o sovraespressa non sono pi`u contraddistinti
dall’ipotesi di scambiabilit`a, ma piuttosto da una distribuzione mistura con un numero
aleatorio di componenti. In questo modo il modello consente di cogliere la presenza di
aspetti di eterogeneit`a conducendo di conseguenza ad un modello bayesiano di clustering
sia per quanto attiene ai geni che alle unit`a. Il modello viene applicato ad un insieme di
dati simulati e ad uno di osservazioni reali
Bayesian analysis of extreme values by mixture modeling
No full textModeling of extreme values in the presence of heterogeneity is still a relatively unexplored area. We consider losses pertaining to several related categories. For each category, we view exceedances over a given threshold as generated by a Poisson process whose intensity is regulated by a specific location, shape and scale parameter. Using a Bayesian approach, we develop a hierarchical mixture prior, with an unknown number of components, for each of the above parameters. Computations are performed using Reversible Jump MCMC. Our model accounts for possible grouping effects and takes advantage of the similarity across categories, both for estimation and prediction purposes. Some guidance on the specification of the prior distribution is provided, together with an assessment of inferential robustness. The method is illustrated throughout using a data set on large claims against a well-known insurance company over a 15-year period
WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools
Full text linkMotivation: As the number of studies looking at differences between DNA methylation increases, there is a growing demand to develop and benchmark statistical methods to analyse these data. To date no objective approach for the comparison of these methods has been developed and as such it remains difficult to assess which analysis tool is most appropriate for a given experiment. As a result, there is an unmet need for a DNA methylation data simulator that can accurately reproduce a wide range of experimental setups, and can be routinely used to compare the performance of different statistical models.
Results: We have developed WGBSSuite, a flexible stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide. Several simulator parameters can be derived directly from real datasets provided by the user in order to mimic real case scenarios. Thus, it is possible to choose the most appropriate statistical analysis tool for a given simulated design. To show the usefulness of our simulator, we also report a benchmark of commonly used methods for differential methylation analysis.
Availability and implementation: WGBS code and documentation are available under GNU licence at http://www.wgbssuite.org.uk/
Contact: [email protected] or [email protected]
Supplementary information:Supplementary data are available at Bioinformatics online
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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