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Introduction to Affymetrix Microarrays

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Presentation on theme: "Introduction to Affymetrix Microarrays"— Presentation transcript:

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

2 Introduction to microarrays Steps in analysis

3 Introduction to microarrays Affymetrix Instrumentation
Design Experiment Prepare Sample Wash& Stain Hybridize Scan Hybridization Oven Fluidics Station Scanner Probe Array Data Analysis Software

4 Introduction to microarrays Chip features

5 Introduction to microarrays Arrays and Applications

6 Introduction to microarrays Affymetrix Applications

7 Introduction to microarrays Development of Affymetrix technology

8 Introduction to microarrays Bioinformatic flowchart

9 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) 8 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

10 Computer Lab Quality Control of data

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