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.

Training and education programs in automatic data processing (ADP).

Mode of access: Internet.

Directory of purchasing offices, Illinois state government, universities and colleges /

Cover title.

The function and needs of schools of education in universities and colleges,

Mode of access: Internet.

Organizational and direct support maintenance manual : data processing unit CP-1435/MYQ-4, (NSN 7010-01-092-2549).

Includes index.

Report of Committee on college entrance requirements July, 1899 : appointed by Departments of secondary education and higher education at Denver meeting July, 1895.

At head of title: National educational association.

Adapting data processing to compare model and experiment accurately: A discrete element model and magnetic resonance measurements of a 3d cylindrical fluidized bed

Discrete element modeling is being used increasingly to simulate flow in fluidized beds. These models require complex measurement techniques to provide validation for the approximations inherent in the model. This paper introduces the idea of modeling the experiment to ensure that the validation is accurate. Specifically, a 3D, cylindrical gas-fluidized bed was simulated using a discrete element model (DEM) for particle motion coupled with computational fluid dynamics (CFD) to describe the flow of gas. The results for time-averaged, axial velocity during bubbling fluidization were compared with those from magnetic resonance (MR) experiments made on the bed. The DEM-CFD data were postprocessed with various methods to produce time-averaged velocity maps for comparison with the MR results, including a method which closely matched the pulse sequence and data processing procedure used in the MR experiments. The DEM-CFD results processed with the MR-type time-averaging closely matched experimental MR results, validating the DEM-CFD model. Analysis of different averaging procedures confirmed that MR time-averages of dynamic systems correspond to particle-weighted averaging, rather than frame-weighted averaging, and also demonstrated that the use of Gaussian slices in MR imaging of dynamic systems is valid. © 2013 American Chemical Society.

Proceedings of the National Association of State Universities and Land-Grant Colleges ... annual Convention.

Title from cover.

Degree programs at universities and four year colleges in Illinois.

Chiefly tables.

Requirements for the bachelor's degree in southern colleges;

Mode of access: Internet.

Quasi-lossless optical links for broad-band transmission and data processing

We present the first experimental implementation of a recently designed quasi-lossless fiber span with strongly reduced signal power excursion. The resulting fiber waveguide medium can be advantageously used both in lightwave communications and in all-optical nonlinear data processing.

Quasi-lossless spans for broadband transmission and data processing

We present the first experimental implementation of a recently designed quasi-lossless fibre span with strongly reduced signal power excursion. The resulting fibre waveguide medium can be advantageously used both in lightwave communications and in all-optical nonlinear data processing.

Quasi-lossless optical links for broad-band transmission and data processing

We present the first experimental implementation of a recently designed quasi-lossless fiber span with strongly reduced signal power excursion. The resulting fiber waveguide medium can be advantageously used both in lightwave communications and in all-optical nonlinear data processing. © 2005 IEEE.