IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.

MOTIVATION: Microarray results accumulated in public repositories are widely reused in meta-analytical studies and secondary databases. The quality of the data obtained with this technology varies from experiment to experiment, and an efficient method for quality assessment is necessary to ensure their reliability. RESULTS: The lack of a good benchmark has hampered evaluation of existing methods for quality control. In this study, we propose a new independent quality metric that is based on evolutionary conservation of expression profiles. We show, using 11 large organ-specific datasets, that IQRray, a new quality metrics developed by us, exhibits the highest correlation with this reference metric, among 14 metrics tested. IQRray outperforms other methods in identification of poor quality arrays in datasets composed of arrays from many independent experiments. In contrast, the performance of methods designed for detecting outliers in a single experiment like Normalized Unscaled Standard Error and Relative Log Expression was low because of the inability of these methods to detect datasets containing only low-quality arrays and because the scores cannot be directly compared between experiments. AVAILABILITY AND IMPLEMENTATION: The R implementation of IQRray is available at: ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R. CONTACT: Marta.Rosikiewicz@unil.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Aplicación para la transformación y estudio de archivos log

La aplicación Log2XML tiene como objeto principal la transformación de archivos log en formato texto con separador de campos a un formato XML estandarizado. Para permitir que la aplicación pueda trabajar con logs de diferentes sistemas o aplicaciones, dispone de un sistema de plantillas (indicación de orden de campos y carácter separador) que permite definir la estructura mínima para poder extraer la información de cualquier tipo de log que se base en separadores de campo. Por último, la aplicación permite el procesamiento de la información extraída para la generación de informes y estadísticas.Por otro lado, en el proyecto se profundiza en la tecnología Grails.

Disseny d'un sistema de log genèric per a la implementació de sistemes operacionals.

Aquest projecte permetrà aprofundir en el coneixement de l'estructura de funcionament del PL/SQL d'Oracle (crides a procediments i, especialment, tractament d'excepcions), en la utilització de JDBC com a mecanisme de comunicació entre JAVA i Oracle, i en l'ús de les classes de generació d'interfícies gràfiques d'usuari (swing) i, a més, permetrà posar en pràctica funcionalitats d'Oracle que no havia tingut oportunitat d'emprar, com ara tipus genèrics de dades, objectes persistents o transaccions autònomes.

Use of high-resolution geophysical data to characterize heterogeneous aquifers: influence of data integration method on hydrological predictions

The integration of geophysical data into the subsurface characterization problem has been shown in many cases to significantly improve hydrological knowledge by providing information at spatial scales and locations that is unattainable using conventional hydrological measurement techniques. The investigation of exactly how much benefit can be brought by geophysical data in terms of its effect on hydrological predictions, however, has received considerably less attention in the literature. Here, we examine the potential hydrological benefits brought by a recently introduced simulated annealing (SA) conditional stochastic simulation method designed for the assimilation of diverse hydrogeophysical data sets. We consider the specific case of integrating crosshole ground-penetrating radar (GPR) and borehole porosity log data to characterize the porosity distribution in saturated heterogeneous aquifers. In many cases, porosity is linked to hydraulic conductivity and thus to flow and transport behavior. To perform our evaluation, we first generate a number of synthetic porosity fields exhibiting varying degrees of spatial continuity and structural complexity. Next, we simulate the collection of crosshole GPR data between several boreholes in these fields, and the collection of porosity log data at the borehole locations. The inverted GPR data, together with the porosity logs, are then used to reconstruct the porosity field using the SA-based method, along with a number of other more elementary approaches. Assuming that the grid-cell-scale relationship between porosity and hydraulic conductivity is unique and known, the porosity realizations are then used in groundwater flow and contaminant transport simulations to assess the benefits and limitations of the different approaches.

Comparing correspondence analysis and the log-ratio alternative for representing categorical data

We compare correspondance análisis to the logratio approach based on compositional data. We also compare correspondance análisis and an alternative approach using Hellinger distance, for representing categorical data in a contingency table. We propose a coefficient which globally measures the similarity between these approaches. This coefficient can be decomposed into several components, one component for each principal dimension, indicating the contribution of the dimensions to the difference between the two representations. These three methods of representation can produce quite similar results. One illustrative example is given

A Log-linear model of grain size influence on the geochemistry of sediments

Sediment composition is mainly controlled by the nature of the source rock(s), and chemical (weathering) and physical processes (mechanical crushing, abrasion, hydrodynamic sorting) during alteration and transport. Although the factors controlling these processes are conceptually well understood, detailed quantification of compositional changes induced by a single process are rare, as are examples where the effects of several processes can be distinguished. The present study was designed to characterize the role of mechanical crushing and sorting in the absence of chemical weathering. Twenty sediment samples were taken from Alpine glaciers that erode almost pure granitoid lithologies. For each sample, 11 grain-size fractions from granules to clay (ø grades &-1 to &9) were separated, and each fraction was analysed for its chemical composition.The presence of clear steps in the box-plots of all parts (in adequate ilr and clr scales) against ø is assumed to be explained by typical crystal size ranges for the relevant mineral phases. These scatter plots and the biplot suggest a splitting of the full grain size range into three groups: coarser than ø=4 (comparatively rich in SiO2, Na2O, K2O, Al2O3, and dominated by “felsic” minerals like quartz and feldspar), finer than ø=8 (comparatively rich in TiO2, MnO, MgO, Fe2O3, mostly related to “mafic” sheet silicates like biotite and chlorite), and intermediate grains sizes (4≤ø &8; comparatively rich in P2O5 and CaO, related to apatite, some feldspar).To further test the absence of chemical weathering, the observed compositions were regressed against three explanatory variables: a trend on grain size in ø scale, a step function for ø≥4, and another for ø≥8. The original hypothesis was that the trend could be identified with weathering effects, whereas each step function would highlight those minerals with biggest characteristic size at its lower end. Results suggest that this assumption is reasonable for the step function, but that besides weathering some other factors (different mechanical behavior of minerals) have also an important contribution to the trend.Key words: sediment, geochemistry, grain size, regression, step function

Aplicación de técnicas de minería de datos a los log generados por CATEDU

Extracción de conocimiento de los log generados por un servidor web aplicando técnicas de minería de datos.

Inequalities for a new data-based method for selecting nonparametric density estimates

We continue the development of a method for the selection of a bandwidth or a number of design parameters in density estimation. We provideexplicit non-asymptotic density-free inequalities that relate the $L_1$ error of the selected estimate with that of the best possible estimate,and study in particular the connection between the richness of the classof density estimates and the performance bound. For example, our methodallows one to pick the bandwidth and kernel order in the kernel estimatesimultaneously and still assure that for {\it all densities}, the $L_1$error of the corresponding kernel estimate is not larger than aboutthree times the error of the estimate with the optimal smoothing factor and kernel plus a constant times $\sqrt{\log n/n}$, where $n$ is the sample size, and the constant only depends on the complexity of the family of kernels used in the estimate. Further applications include multivariate kernel estimates, transformed kernel estimates, and variablekernel estimates.

Avaliação do acesso a periódicos eletrônicos na web pela análise do arquivo de log de acesso

Este artigo apresenta uma abordagem sobre a avaliação do acesso a periódicos eletrônicos disponibilizados na World Wide Web por meio da análise do arquivo de log de acesso. O arquivo de log de acesso da revista Informação & Sociedade: Estudos é processado e apresentado como um exemplo de aplicação do uso de uma ferramenta automatizada de análise para arquivo de iog de acesso. As características inerentes à análise do arquivo de log de acesso são apresentadas e discutidas.

Long-term impacts of forest harvesting related soil disturbance on log product yields and economic potential in a New Zealand forest

Abstract