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检索条件"任意字段=Microarrays: Optical Technologies and Informatics"

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microarrays: optical technologies and informatics: 21-22 January 2001, San Jose, USA

Microarrays: Optical Technologies and Informatics: 21-22 Jan...

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2001年

作者： Yidong Chen Edward R Dougherty A N Dorsel

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Proceedings of SPIE: microarrays: optical technologies and informatics

Proceedings of SPIE: Microarrays: Optical Technologies and I...

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microarrays: optical technologies and informatics

This Volume 4266 of the conference proceedings contains 27 papers. Topics discussed include microarrays, optical technologies and informatics, image data analysis, detecting signals, data normalization and quality con... 详细信息

关键词： optical data processing

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Normalization and error estimation for biomolecular expression patterns

Normalization and error estimation for biomolecular expressi...

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Conference on microarrays - optical technologies and informatics

作者： Luck, S Dupont Co Inc Agr Biotechnol Genomics Newark DE 19714 USA

ISBN: (纸本)0819439444

We describe methods for the analysis expression patterns based on a vector representation for intensities. Normalization for multiple experiments is iterative and is obtained by identifying a vector that optimally correlates expression patterns. Error estimates for intensities are obtained by analyzing deviations in expression relative to the correlation vector. A normalization method for applying corrections from spiked, two-color fluorescence measurements is also described.

关键词： biomolecular expression normalization error analysis microarrays

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Sophisticated lenses for microarray analysis

Sophisticated lenses for microarray analysis

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Conference on microarrays - optical technologies and informatics

作者： Guse, F Bleicher, J A LINOS Co Rodenstock Prazisionsopt D-80469 Munich Germany

ISBN: (纸本)0819439444

The correct choice of the optical system is of major importance for the performance of microarray analysis instruments based on fluorescence. A variety of different approaches is possible. The basic concepts are (a) imaging of an extended field on a spatially resolving detector, (b) scanning the microarray with a flat-field lens and (c) scanning by laterally shifting a confocal optical system. Depending on the approach, the optical system may range from a lightweight lens of a few gramms to a heavy system with a hundred millimetres in diameter. Further this determines the achievable optical performance in terms of spatial resolution on the microarray and the numerical aperture. Whereas by increasing the numerical aperture more fluorescent photons are captured, a higher spatial resolution avoids cross-talking between spots. But only considering the optics will not render the most efficient concept. The optical system is an integrated part in a number of complex, challenging components. Therefore, the requirements on the optics have often to be balanced with other system specific constraints. A custom-tailored optical design for an instrument under development allows the best compromise and is hereby a fundamental step to achieve maximum overall performance.

关键词： microarrays lens design scanning confocal microscopy fluorescence

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A modified confocal scanner system for microarrays

A modified confocal scanner system for microarrays

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Conference on microarrays - optical technologies and informatics

作者： Hsu, IC Chen, R Chen, YL Natl Tsing Hua Univ Dept Atom Sci Hsinchu 300 Taiwan

ISBN: (纸本)0819439444

Based on the original design of the confocal scanner system by Dr. Eisen and his colleagues at Stanford Univ., we have developed a modified confocal scanner system. The modified scanner only used one PMT instead of two PMTs in its precedent one. About half of the dichroic beamsplitters were replaced by reflection mirrors in the modified system. Therefore, we will be able to reduce the power of laser by a fact of 1.5. It will enhance the stability of the laser power and increase the accuracy of the detection system. The size of the modified system was decreased due to the simplified optics system. The optical system and the preliminary scanning results of this modified confocal scanner system will be presented in this paper. We will also discuss some possible further improvement of the system.

关键词： laser scan confocal Microarray fluorescence DNA chips scanner

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Designing oligo libraries taking alternative splicing into account

Designing oligo libraries taking alternative splicing into a...

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Conference on microarrays - optical technologies and informatics

作者： Shoshan, A Grebinskiy, V Magen, A Scolnicov, A Fink, E Lehavi, D Wasserman, A Compugen Inc Jamesburg NJ 08831 USA

ISBN: (纸本)0819439444

We have designed sequences for DNA microarrays and oligo libraries, taking alternative splicing into account. Alternative splicing is a common phenomenon, occurring in more than 35% of the human genes. In many cases, different splice variants have different functions, are expressed in different tissues or may indicate different stages of disease. When designing sequences for DNA microarrays or oligo libraries, it is very important to take into account the sequence information of all the mRNA transcripts. Therefore, when a gene has more than one transcript (as a result of alternative splicing, alternative promoter sites or alternative poly-adenylation sites), it is very important to take all of them into account in the design. We have used the LEADS transcriptome prediction system to cluster and assemble the human sequences in GenBank and design optimal oligonucleotides for all the human genes with a known mRNA sequence based on the LEADS predictions.

关键词： DNA microarrays probe design alternative splicing EST clustering chip design

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Statistical issues in signal extraction from microarrays

Statistical issues in signal extraction from microarrays

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Conference on microarrays - optical technologies and informatics

作者： Bergemann, T Quiaoit, F Delrow, J Zhao, LP Fred Hutchinson Canc Res Ctr Div Publ Hlth Sci Seattle WA 98109 USA

ISBN: (纸本)0819439444

Microarray technologies are increasingly used in biomedical research to study genome-wide expression profiles in the post genomic era. Their popularity is largely due to their high throughput and economical affordability. For example, microarrays have been applied to studies of cell cycle, regulatory circuitry, cancer cell lines, tumor tissues, and drug discoveries. One obstacle facing the continued success of applying microarray technologies, however, is the random variation present on microarrays: within signal spots, between spots and among chips. In addition, signals extracted by available software packages seem to vary significantly. Despite a variety of software packages, it appears that there are two major approaches to signal extraction. One approach is to focus on the identification of signal regions and hence estimation of signal levels above background levels. The other approach is to use the distribution of intensity values as a way of identifying relevant signals. Building upon both approaches, the objective of our work is to develop a method that is statistically rigorous and also efficient and robust. Statistical issues to be considered here include: (1) how to refine grid alignment so that the overall variation is minimized, (2) how to estimate the signal levels relative to the local background levels as well as the variance of this estimate, and (3) how to integrate red and green channel signals so that the ratio of interest is stable, simultaneously relaxing distributional assumptions.

关键词： image analysis image segmentation microarray signal extraction spatial statistics

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A random signal model for cDNA microarrays

A random signal model for cDNA microarrays

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Conference on microarrays - optical technologies and informatics

作者： Balagurunathan, Y Dougherty, ER Chen, YD Bittner, ML Trent, JM Texas A&M Univ Dept Elect Engn College Stn TX 77843 USA

ISBN: (纸本)0819439444

The images resulting from cDNA microarrays are highly random. There are many aspects to this randomness, including spot size, shape, intensity, uniformity, and circularity, as well as both foreground and background noise. This paper presents a random model for the generation of microrarray images. The model is complicated and contains over twenty parameters. It can be used to test microarray imaging algorithms and to simulate the effects of various dependencies within the image formation process.

关键词： random model simulated cDNA microarray cDNA spot model

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Rank-based algorithms for analysis of microarrays

Rank-based algorithms for analysis of microarrays

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Conference on microarrays - optical technologies and informatics

作者： Liu, WM Mei, R Bartell, DM Di, XJ Affymetrix Inc Santa Clara CA 95051 USA

ISBN: (纸本)0819439444

Analysis of microarray data often involves extracting information from raw intensities of spots or cells and making certain calls. Rank-based algorithms are powerful tools to provide probability values of hypothesis tests, especially when the distribution of the intensities is unknown. For our current gene expression arrays, a gene is detected by a set of probe pairs consisting of perfect match and mismatch cells. The one-sided upper-tail Wilcoxon's signed rank test is used in our algorithms for absolute calls (whether a gene is detected or not), as well as comparative calls (whether a gene is increasing or decreasing or no significant change in a sample compared with another sample). We also test the possibility to use only perfect match cells to make calls. This paper focuses on absolute calls. We have developed error analysis methods and software tools that allow us to compare the accuracy of the calls in the presence or absence of mismatch cells at different target concentrations. The usage of nonparametric rank-based tests is not limited to absolute and comparative calls of gene expression chips. They can also be applied to other oligonucleotide microarrays for genotyping and mutation detection, as well as spotted arrays.

关键词： algorithm gene expression microarray nonparametric method rank

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A groundtruth approach to accurate quantitation of fluorescence microarrays

A groundtruth approach to accurate quantitation of fluoresce...

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Conference on microarrays - optical technologies and informatics

作者： Kegelmeyer, LM Tomascik-Cheeseman, L Burnett, MS van Hummelen, P Wyrobek, AJ Lawrence Livermore Natl Lab Livermore CA 94550 USA

ISBN: (纸本)0819439444

To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results substantially closer to the known groundtruth for these samples.

关键词： groundtruth cDNA quantitative expression fluorescence microarrays

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