Affymetrix

##Introduction and Instructions

Welcome to the Affymetrix Tutorial. This tutorial will guide you through a basic Affymetrix experiment using freely available Affymetrix microarray data from Gene Expression Omnibus (GEO). Below is the recommended progression for advancing through this tutorial:

(1) Go through the Shared Features page to familiarize yourself with the methods shared across all microarray experiments
(2) Return to this page to go through the annotated code along with accompanying tutorial slides to become acquainted with a typical Affymetrix microarray experiment
(3) Download Affymetrix.R to work through the tutorial directly on your own computer/server
(4) Use Affymetrix.R as a template for your own Affymetrix microarray experiment, and refer to the annotated code and tutorial slides as needed

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Tutorial Slides

In the future, this page will hold links to the more useful slides that accompany this presentation

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Annotated Code

####Experiment Progression

Here are the steps for a basic Affymetrix microarray experiment:

[1. Get Data](####1. Get Data)
[2. QC on Non-Normalized Data](####2. QC on Non-Normalized Data)
[3. Normalization](####3. Normalization)
[4. Batch Correction](####4. Batch Correction)
[5. Outlier Removal](####5. Outlier Removal)
[6. QC on Normalized Data](####6. QC on Normalized Data)
[7. Covariate Analysis](####7. Covariate Analysis)
[8. Annotating Probes](####8. Annotating Probes)
[9. Collapse Rows](####9. Collapse Rows)
[10. Differential Expression Analysis](####10. Differential Expression Analysis)

####1. Get Data

####2. QC on Non-Normalized Data

####3. Normalization

####4. Batch Correction

####5. Outlier Removal

####6. QC on Normalized Data

####7. Covariate Analysis

####8. Annotating Probes

####9. Collapse Rows

####10. Differential Expression Analysis