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Statistical estimation of gene expression using multiple laser scans of microarrays.

Khondoker, MR; Glasbey, CA; Worton, BJ; (2006) Statistical estimation of gene expression using multiple laser scans of microarrays. Bioinformatics , 22 (2) pp. 215-219. 10.1093/bioinformatics/bti790.

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Abstract

UNLABELLED: We propose a statistical model for estimating gene expression using data from multiple laser scans at different settings of hybridized microarrays. A functional regression model is used, based on a non-linear relationship with both additive and multiplicative error terms. The function is derived as the expected value of a pixel, given that values are censored at 65 535, the maximum detectable intensity for double precision scanning software. Maximum likelihood estimation based on a Cauchy distribution is used to fit the model, which is able to estimate gene expressions taking account of outliers and the systematic bias caused by signal censoring of highly expressed genes. We have applied the method to experimental data. Simulation studies suggest that the model can estimate the true gene expression with negligible bias. AVAILABILITY: FORTRAN 90 code for implementing the method can be obtained from the authors.

Type: Article
Title: Statistical estimation of gene expression using multiple laser scans of microarrays.
Location: England
DOI: 10.1093/bioinformatics/bti790
Keywords: Algorithms, Data Interpretation, Statistical, Gene Expression Profiling, Image Interpretation, Computer-Assisted, In Situ Hybridization, Fluorescence, Microscopy, Confocal, Microscopy, Fluorescence, Models, Genetic, Models, Statistical, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, Sensitivity and Specificity, Software
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Pop Health Sciences > Institute of Epidemiology and Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Pop Health Sciences > Institute of Epidemiology and Health > Applied Health Research
URI: http://discovery.ucl.ac.uk/id/eprint/1484486
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