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](Affymetrix##Annotated Code) along with accompanying [tutorial slides] (Affymetrix##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