Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.

Data Processing Student Working

A student from the Data Processing program at the New York Trade School is shown working. Black and white photograph with some edge damage due to writing in black along the top.

Felice Gigante, Data Processing Customer Engineer

Felice Gigante a graduate from the New York Trade School Electronics program works on a machine in his job as Data Processing Customer Engineer for the International Business Machines Corp. Original caption reads, "Felice Gigante - Electronices, International Business Machines Corp." Black and white photograph with caption glued to reverse.

CMS data processing workflows during an extended cosmic ray run

The CMS Collaboration conducted a month-long data taking exercise, the Cosmic Run At Four Tesla, during October-November 2008, with the goal of commissioning the experiment for extended operation. With all installed detector systems participating, CMS recorded 270 million cosmic ray events with the solenoid at a magnetic field strength of 3.8 T. This paper describes the data flow from the detector through the various online and offline computing systems, as well as the workflows used for recording the data, for aligning and calibrating the detector, and for analysis of the data. © 2010 IOP Publishing Ltd and SISSA.

The impact of adding SBAS data on GPS data processing in southeast of Brazil: Preliminary result

Nowadays, L1 SBAS signals can be used in a combined GPS+SBAS data processing. However, such situation restricts the studies over short baselines. Besides of increasing the satellite availability, SBAS satellites orbit configuration is different from that of GPS. In order to analyze how these characteristics can impact GPS positioning in the southeast area of Brazil, experiments involving GPS-only and combined GPS+SBAS data were performed. Solutions using single point and relative positioning were computed to show the impact over satellite geometry, positioning accuracy and short baseline ambiguity resolution. Results showed that the inclusion of SBAS satellites can improve the accuracy of positioning. Nevertheless, the bad quality of the data broadcasted by these satellites limits their usage. © Springer-Verlag Berlin Heidelberg 2012.

Preliminary draft of the sections of the CELADE 1980-83 proposal to UNFPA on subprogramme 6: documentation and data processing (INFOPAL, DOCPAL) (for discussion only; not to be quoted)

El Sub-Programa de Documentacion en Poblacion y Procesamiento de Datos del CELADE se compone de tres elementos que corresponden a los primeros objetivos inmediatos del mismo: el Sistema de Documentacion en Poblacion para America Latina (DOCPAL), el Banco de Datos y la Unidad de Procesamiento de Informacion. El presente documento describe los objetivos, antecedentes y justificacion de cada uno de estos tres nucleos, asi como las actividades contempladas para el periodo 1980-1983 y que fundamentan el presupuesto contenido en la solicitud de fondos al UNFPA

Electronic Data Interchange (EDI): development activities in selected countries of the Americas

This issue describes progress in EDI in Argentina, Brazil, Chile, Mexico, the United States and Venezuela up to August 1996. The information is based on the progress reports prepared by country representatives for the Pan-American EDIFACT Board (PAEB), which coordinates EDI development activities in the Americas.

Electronic data interchange in port management: the experience of the port of Barcelona

Every port is unique. Although all ports exist for the same basic purpose (to act as an interface in the transfer from one mode of transport to another), no two are ever organized in the same way.Ports may be classified according to: Physical conditions: location (geographical position, man-made or natural harbour, estuary location, difficult weather conditions, tides, etc.) and size (large, small or medium-sized). Use: commercial (general cargo, bulk solids, bulk liquids, oil, break bulk, mixed), passenger, sport and leisure, fishing, mixed, etc. Ownership: private, municipal, regional or State-owned. The Port Authority's role in management of the port: Overall control, i.e. the Port Authority plans, sets up and operates the whole range of services. Facilitator, i.e. the Port Authority plans and sets up the infrastructure and the superstructure, but services are provided by private companies. Landlord, i.e. the Port Authority allows private companies to be responsible for the superstructure and provide port services. Different combinations of port types will therefore give rise to different kinds of organization and different information flows, which means that the associated information systems may differ significantly from port to port. Since this paper relates to the port of Barcelona, with its own specific characteristics, the contents may not always be applicable to other ports.

Teds-easy - descrição automática de transducer electronic data sheet

Pós-graduação em Engenharia Elétrica - FEIS

Quantitative proteome analysis in cardiovascular physiology and pathology. I. Data processing

Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. It has been found that the silver-stained readout offers a convenient approach for quantitation if a linear range for gel loading is defined. In addition, a broad range of a 10-fold input (loading 20-200 microg per gel) fulfills the linearity criteria, although at the lowest input (20 microg) a portion of protein species will remain undetected. The method is reliable and reproducible within a range of 65-200 microg input. The normalization procedure using the sum of all spot intensities from a silver-stained 2D pattern has been shown to be less reliable than other approaches, namely, normalization through median or through involvement of interquartile range. A special refinement of the normalization through virtual segmentation of pattern, and calculation of normalization factor for each stratum provides highly satisfactory results. The presented results not only provide evidence for the usefulness of silver-stained gels for quantitative evaluation, but they are directly applicable to the research endeavor of monitoring alterations in cardiovascular pathophysiology.