An Opinionated Guide to Microarray Data Analysis

Mark Reimers
Department of Biostatistics
Virginia Commonwealth University

N.B. This site is under construction.
If you don't find what you want please check back in a few months. In the mean time, suggestions for topics to be included are welcome!

This site is meant to be a companion to an article in PLoS Comp. Bio. to appear

In the mean time here are some resources:

Slides from the 2008 ISMB Tutorial on Microarray Data Analysis

Handout from the 2008 ISMB Tutorial on Microarray Data Analysis

and the older version of this Guide

This site discusses methods to address the important practical issues in microarray data analysis, based on my experience with hundreds of data sets and on discussions with other microarray statisticians. The focus here is not on sophisticated algorithms but on practical issues that most researchers encounter in the course of a microarray study. As the title suggests, this guide will give direct advice rather than making cautious suggestions typical of the scientific literature.

This site is organized as follows

Designing a microarray experiment

Image Analysis

Quality assessment of arrays

Normalization: making raw data comparable

Summarization: getting the best estimates when each feature has several probes

Exploratory analysis of processed data

Selecting Genes: significance tests for individual genes or loci

Pathway Analyses: tests using gene sets

Solexa data analysis New! Comments and questions to

Additional Contributors:

Jiayi Hou (Normalization)

Mercer Thorp (Image analysis)