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
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
Estimates of
Abundance (methods for combining data from multiple probes to get single
estimates)
Downstream Analysis
For descriptions of the technology
see TECH LINKS