title: Analysis of whole-genome microarray replicates using mixed models.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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).
authors.affiliation: School of Crystallography, Birkbeck College, London WC1E 7HX, UK. l.wernisch@bbk.ac.uk
authors.forename: Lorenz
authors.initials: L
authors.lastname: Wernisch
authors.forename: Sharon L
authors.initials: SL
authors.lastname: Kendall
authors.forename: Shamit
authors.initials: S
authors.lastname: Soneji
authors.forename: Andreas
authors.initials: A
authors.lastname: Wietzorrek
authors.forename: Tanya
authors.initials: T
authors.lastname: Parish
authors.forename: Jason
authors.initials: J
authors.lastname: Hinds
authors.forename: Philip D
authors.initials: PD
authors.lastname: Butcher
authors.forename: Neil G
authors.initials: NG
authors.lastname: Stoker
mesh_terms: D000465:Algorithms; D000704:Analysis of Variance; D002478:Cells, Cultured; D004269:DNA, Bacterial / Q000032:analysis / Q000145:classification / Q000235:genetics*; D029721:Drosophila Proteins; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D016297:Mutagenesis, Site-Directed; D009169:Mycobacterium tuberculosis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017346:Protein Serine-Threonine Kinases / Q000235:genetics*; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D004269:DNA, Bacterial; D029721:Drosophila Proteins; C419769:trc protein, Drosophila; D017346:Protein Serine-Threonine Kinases