An (Opinionated) Guide to Microarray Data Analysis

Mark Reimers,

Karolinska Instutitute, Dept. of Biosciences

The aim of these pages is to set out the author’s opinions about the best ways to deal with the most common issues in microarray data analysis. The opinions are based on experience with dozens of collaborating lab scientists, and discussions with microarray statisticians. Contributions, disputes, and opinions are welcome (and may be posted!). These pages are intended primarily for people working in a microarray facility. However I hope that statisticians and programmers will also find interesting material here.

This site is organized as follows

General Issues

Experimental design

Distributions and transforms

Approaches to Normalization

Spotted Array Issues (two-color competitively hybridized microarrays)

Image analysis for spotted arrays (not done)

Quality control of spotted arrays

Normalization of spotted arrays


Affymetrix Issues

Quality control


Estimates of Abundance (methods for combining data from multiple probes to get single estimates)


Downstream Analysis



Statistical Significance


For descriptions of the technology see TECH LINKS