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Probabilistic estimation of microarray data reliability and underlying gene expression
BACKGROUND: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address these issues by an information theoretic approach, applied to d...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2003
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC222958/ https://www.ncbi.nlm.nih.gov/pubmed/12967349 http://dx.doi.org/10.1186/1471-2105-4-40 |
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author | Bilke, Sven Breslin, Thomas Sigvardsson, Mikael |
author_facet | Bilke, Sven Breslin, Thomas Sigvardsson, Mikael |
author_sort | Bilke, Sven |
collection | PubMed |
description | BACKGROUND: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address these issues by an information theoretic approach, applied to discretized expression values in replicated gene expression data. RESULTS: Our approach yields a quantitative measure of two important parameter classes: First, the probability P(σ|S) that a gene is in the biological state σ in a certain variety, given its observed expression S in the samples of that variety. Second, sample specific error probabilities which serve as consistency indicators of the measured samples of each variety. The method and its limitations are tested on gene expression data for developing murine B-cells and a t-test is used as reference. On a set of known genes it performs better than the t-test despite the crude discretization into only two expression levels. The consistency indicators, i.e. the error probabilities, correlate well with variations in the biological material and thus prove efficient. CONCLUSIONS: The proposed method is effective in determining differential gene expression and sample reliability in replicated microarray data. Already at two discrete expression levels in each sample, it gives a good explanation of the data and is comparable to standard techniques. |
format | Text |
id | pubmed-222958 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2003 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-2229582003-10-24 Probabilistic estimation of microarray data reliability and underlying gene expression Bilke, Sven Breslin, Thomas Sigvardsson, Mikael BMC Bioinformatics Methodology Article BACKGROUND: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address these issues by an information theoretic approach, applied to discretized expression values in replicated gene expression data. RESULTS: Our approach yields a quantitative measure of two important parameter classes: First, the probability P(σ|S) that a gene is in the biological state σ in a certain variety, given its observed expression S in the samples of that variety. Second, sample specific error probabilities which serve as consistency indicators of the measured samples of each variety. The method and its limitations are tested on gene expression data for developing murine B-cells and a t-test is used as reference. On a set of known genes it performs better than the t-test despite the crude discretization into only two expression levels. The consistency indicators, i.e. the error probabilities, correlate well with variations in the biological material and thus prove efficient. CONCLUSIONS: The proposed method is effective in determining differential gene expression and sample reliability in replicated microarray data. Already at two discrete expression levels in each sample, it gives a good explanation of the data and is comparable to standard techniques. BioMed Central 2003-09-10 /pmc/articles/PMC222958/ /pubmed/12967349 http://dx.doi.org/10.1186/1471-2105-4-40 Text en Copyright © 2003 Bilke et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Methodology Article Bilke, Sven Breslin, Thomas Sigvardsson, Mikael Probabilistic estimation of microarray data reliability and underlying gene expression |
title | Probabilistic estimation of microarray data reliability and underlying gene expression |
title_full | Probabilistic estimation of microarray data reliability and underlying gene expression |
title_fullStr | Probabilistic estimation of microarray data reliability and underlying gene expression |
title_full_unstemmed | Probabilistic estimation of microarray data reliability and underlying gene expression |
title_short | Probabilistic estimation of microarray data reliability and underlying gene expression |
title_sort | probabilistic estimation of microarray data reliability and underlying gene expression |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC222958/ https://www.ncbi.nlm.nih.gov/pubmed/12967349 http://dx.doi.org/10.1186/1471-2105-4-40 |
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