Microarray Analysis - The Basics

Microarray AnalysisThe BasicsThomas GirkeDecember 9, 2011 Microarray AnalysisSlide 1/42 TechnologyChallengesData AnalysisData DepositoriesR and BioConductorHomework AssignmentMicroarray AnalysisSlide 2/42 OutlineTechnologyChallengesData AnalysisData DepositoriesR and BioConductorHomework AssignmentMicroarray AnalysisTechnologySlide 3/42 Microarray 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 4/42 Why Microarrays?

e.g. real-time PCR and analysis of transgenics or mutants Choose type of experiment common reference, e.g.: S1 x S1+T1, S1 x S1+T2 paired references, e.g.: S1 x S1+T1, S2 x S2+T1 loop & pooling designs many other designs At least three (two) biological replicates are essential Biological replicates: utilize independently collected biosamples

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