MOTIVATION: Microarray studies permit to quantify expression levels on a global scale by measuring transcript abundance of thousands of genes simultaneously. A difficulty when analysing expression measures is how to model variability for the whole set of genes. It is usually unrealistic to assume a common variance for each gene. Several approaches to model gene-specific variances are proposed. We take advantage of calibration experiments, in which the probes hybridized on the two channels come from the same population (self-self experiment). In this case it is possible to estimate the gene-specific variance, to be incorporated in comparative experiments on the same tissue, cellular line or species. RESULTS: We present two approaches to introduce prior information on gene-specific variability from a calibration experiment: an empirical Bayes model and a full Bayesian hierarchical model. We apply the methods in the analysis of human lipopolysaccharide-stimulated leukocyte experiments. AVAILABILITY: The calculations are implemented in WinBugs. The codes are available on request from the authors.

Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data / M.Blangiardo; S.Toti; B.Giusti; R.Abbate; A.Magi; F.Poggi; L.Rossi; F.Torricelli; A.Biggeri.. - In: BIOINFORMATICS. - ISSN 1367-4803. - STAMPA. - 22:(2006), pp. 50-57.

Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data.

BLANGIARDO, MARTA ANGELA;TOTI, SIMONA;GIUSTI, BETTI;ABBATE, ROSANNA;MAGI, ALBERTO;ROSSI, LUCIANA;TORRICELLI, FRANCESCA;BIGGERI, ANNIBALE
2006

Abstract

MOTIVATION: Microarray studies permit to quantify expression levels on a global scale by measuring transcript abundance of thousands of genes simultaneously. A difficulty when analysing expression measures is how to model variability for the whole set of genes. It is usually unrealistic to assume a common variance for each gene. Several approaches to model gene-specific variances are proposed. We take advantage of calibration experiments, in which the probes hybridized on the two channels come from the same population (self-self experiment). In this case it is possible to estimate the gene-specific variance, to be incorporated in comparative experiments on the same tissue, cellular line or species. RESULTS: We present two approaches to introduce prior information on gene-specific variability from a calibration experiment: an empirical Bayes model and a full Bayesian hierarchical model. We apply the methods in the analysis of human lipopolysaccharide-stimulated leukocyte experiments. AVAILABILITY: The calculations are implemented in WinBugs. The codes are available on request from the authors.
2006
22
50
57
M.Blangiardo; S.Toti; B.Giusti; R.Abbate; A.Magi; F.Poggi; L.Rossi; F.Torricelli; A.Biggeri.
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Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/388496
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