Transcript Slide 1
Introduction to Affymetrix Microarrays Why use microarrays? Permits expression profiling of thousands of genes in parallel Why use Affymetrix microarrays? • • • • • Well established platform Arrays for various species Enables combination of different applications Support from the bioinformatic community Well annoted probesets Introduction to microarrays Steps in analysis Introduction to microarrays Affymetrix Instrumentation Design Experiment Prepare Sample Probe Array Hybridize Wash & Stain Hybridization Oven Fluidics Station Scan Scanner Data Analysis Software Introduction to microarrays Chip features Introduction to microarrays Arrays and Applications Copy Number Changes • WG SNP Mapping Arrays Differential Gene Expression • Exon Arrays • 3’ IVT Expression Arrays Mitochondrial Mutations • Mito Resequencing Genotyping • WG SNP Mapping Arrays • Targeted Genotyping Arrays Somatic Mutations • Targeted Genotyping Arrays • CustomSeq Resequencing Arrays Splice Variant Analysis • Exon Arrays Changes in Methylation Patterns • Whole Genome Tiling Arrays • Promoter Tiling Arrays Introduction to microarrays Affymetrix Applications Introduction to microarrays Development of Affymetrix technology Introduction to microarrays Bioinformatic flowchart Experimental Planning - Variance estimation - Level of significance - How many replicates? Low-level analysis - Background correction - Normalization - Summarization Quality Control - GCOS internal controls - Various methods in R / BioConductor Statistical methods - Pairwise comparisons - Significance testing (t-test, SAM etc) - Clustering - Classification & Prediction Functional Analysis - Pathways - GeneOntologies - Diseases - Motifs - Toxicogenomics - Pharmacogenomics …. Computer Lab -in silico microarray study Title: Molecular profiling of tumor progression in NSCLC Geo id: GSE7880 Array: Affymetrix Human HG-Focus Target Array Design: Primary Recurrent stage IIIB or IV Adenocarcinoma (AC) 10 15 Squamous cell carcinoma (SCC) 10 8 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7880 Lab tasks: • • • • Download data set from GEO Add annotations from Affymetrix Perform t-tests to compare expression between groups Answer a set of questions using web resources Computer Lab Quality Control of data