Revision as of 14:10, 14 August 2006

Basic Microarray Analysis with geWorkbench

Background

Correct and complete microarray analysis requires both an understanding of the actual experiment and the statistical and mathmatical tools being used. The tools and techniques being used will vary depending on the type of experiment and what knowledge the user hopes to gain from the experiment. Here we will describe a how to go about analyzing one of the most common types of microarray experiments - differential gene expression on Affymetrix arrays. Most of the techniques described should be suitable for other types of analysis when appropriately modified, but the user is cautioned against applying them blindly to their own data.

Introduction

Overview of Microarray Analysis

1. Getting Started
   1. Requirements (Windows/Mac/Linux OS, Java 1.5 installed, at least 512 MB RAM)
   2. Installation Download
2. Preparing the Data
   1. From Excel XLS files
   2. From CEL files
3. Load the data
   1. Batch loading of Excel Files
   2. Loading of a single CEL derived geWorkbench file
4. Inspect the data
5. Normalize
6. T-Test
7. GO Analysis
8. Promoter Analysis
9. Pattern Discovery
10. Other Analysis