Analysis of whole-genome microarray replicates using mixed models
| Autor: | Tanya Parish, Philip D. Butcher, Lorenz Wernisch, Shamit Soneji, Jason Hinds, Neil G. Stoker, Sharon L. Kendall, Andreas Wietzorrek |
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| Rok vydání: | 2002 |
| Předmět: |
Statistics and Probability
Mixed model DNA Bacterial Quality Control Microarray Computer science Computational biology Protein Serine-Threonine Kinases computer.software_genre Biochemistry Sensitivity and Specificity Downregulation and upregulation Replication (statistics) Drosophila Proteins Humans Molecular Biology Gene Bootstrapping (statistics) Cells Cultured Oligonucleotide Array Sequence Analysis Analysis of Variance Models Statistical Models Genetic Reproducibility of Results Replicate Gene Expression Regulation Bacterial Mycobacterium tuberculosis Missing data Computer Science Applications Data set Computational Mathematics Noise Computational Theory and Mathematics Gene chip analysis Mutagenesis Site-Directed Data mining computer Algorithms Genome Bacterial |
| Zdroj: | Bioinformatics (Oxford, England). 19(1) |
| ISSN: | 1367-4803 |
| Popis: | Motivation: Microarray experiments are inherently noisy. Replication is the key to estimating realistic fold-changes despite such noise. In the analysis of the various sources of noise the dependency structure of the replication needs to be taken into account. Results: We analyzed replicate data sets from a Mycobacterium tuberculosis trcS mutant in order to identify differentially expressed genes and suggest new methods for filtering and normalizing raw array data and for imputing missing values. Mixed ANOVA models are applied to quantify the various sources of error. Such analysis also allows us to determine the optimal number of samples and arrays. Significance values for differential expression are obtained by a hierarchical bootstrapping scheme on scaled residuals. Four highly upregulated genes, including bfrB, were analyzed further. We observed an artefact, where transcriptional readthrough from these genes led to apparent upregulation of adjacent genes. Availability: All methods and data discussed are available in the package YASMAhttp://www.cryst.bbk.ac.uk/wernisch/yasma.html for the statistical data analysis system R (http://www.R-project.org). Contact: l.wernisch@bbk.ac.uk * To whom correspondence should be addressed. |
| Databáze: | OpenAIRE |
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