Contents

PART I: Introduction (pdf 4 MB)
WEB extra (09.01. 2006, pdf 0.5 MB)

1. Introduction

2. Affymetrix GeneChip system

3. Genotyping systems

4. Image analysis

5. Overview of data analysis

6. Experimental design

7. Reporting results (presentation 4.5. 2006)

8. Basic statistics

   PART II: Analysis (pdf 7.4 MB)
   WEB extra (09.01. 2006, pdf 0.2 MB)

9. Preprocessing of data

10. Normalization

11. Finding differentially expressed genes

12. Cluster analysis of microarray information

    PART III: Data mining (pdf 0.3 MB)
    WEB extra (09.01. 2006, pdf 0.5 MB)

13. Gene regulatory networks

14. Data mining for promoter sequences

15. Biological sequence annotations

16. Software issues

Options:

• Order a printed version of the book online.
• Download the printed book as pdf (12 MB)
• Download the additional web material as pdf (1.3 MB)
• Select relevant parts from above and download or view them separately

A guidebook for DNA Microarray Data Analysis

This guidebook is written in collaboration between several Finnish researchers from different universities and research institutions. The first edition of the DNA microarray data analysis guidebook was written by M. Minna Laine, Tomi Pasanen, Janna Saarela, Ilana Saarikko, Teemu Toivanen, Martti Tolvanen, Jarno Tuimala, Mauno Vihinen, and Garry Wong.

For the second edition, Iiris Hovatta, Katja Kimppa, Antti Lehmussola, Juha Saharinen, and Pekka Tiikkainen joined the writer team.

The purpose of this book is to serve as course and teaching material to introduce basic concepts of microarray data analysis. We hope that especially researchers starting their data analysis can benefit from the book.

This is the second, revised and slightly expanded edition of the DNA microarray data analysis guidebook. As a change to the previous edition, some relatively quickly changing material such as software tutorials have been exclusively published here, on the book's web site. This allows us better keep the material up to date. Please follow links on the Contents part above to access the extra material (all as PDF files).

We are very interested in receiving feedback about this publication. Especially, if you feel that some essential technique has been missed, let us know. Please send your comments to the e-mail address  Jarno.Tuimala at csc.fi.

Copyright

CSC - the Finnish IT center for science, is a non-profit organization for high-performance computing and networking in Finland. CSC is owned by the Ministry of Education. CSC provides cross-disciplinary expertise, computational resources and fast network connections for computational science and engineering.

All rights reserved by CSC - Scientific Computing Ltd., Finland. The PDF version of this book or parts of it can be used for academic non-profit purposes, provided that this copyright notice is included. This publication may not be sold or included as part of other publications without permission of CSC.