Microarray Analysis - The Basics

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Microarray AnalysisThe BasicsThomas GirkeDecember 9, 2011Microarray AnalysisSlide 1/42TechnologyChallengesData AnalysisData DepositoriesR and BioConductorHomework AssignmentMicroarray AnalysisSlide 2/42OutlineTechnologyChallengesData AnalysisData DepositoriesR and BioConductorHomework AssignmentMicroarray AnalysisTechnologySlide 3/42Microarray and Chip TechnologyDefinitionHybridization-based technique that allows simultaneousanalysis of thousands of samples on a solid ProfilingGene copy numberResequencingGenotypingSingle-nucle otide polymorphismDNA-protein interaction ( : ChIP-on-chip)Gene discovery ( : Tiling arrays)Identification of new cell technologiesProtein arraysCompound arraysMicroarray AnalysisTechnologySlide 4/42Why Microarrays?Simultaneous Analysis of thousands of genesDiscovery of gene functionsGenome-wide network analysisAnalysis of mutants and transgenicsIdentification of drug targetsCausal understanding of diseasesClinical studies and field trialsMicroarray AnalysisTechnologySlide 5/42Different Types of MicroarraysSingle channel approachesAffymetrix gene chipsMacroarraysMultiple channel approachesDual color (cDNA) microarra

Develop validation and follow-up strategy for expected expression hits ... content normalization linear model RMA array quantile / robust t of background normalization linear model ... Why Using R and BioConductor for Array Analysis? Complete statistical package and programming language Useful for all bioscience areas

  Analysis, Basics, Model, Validation, Statistical, Microarray, Microarray analysis the basics