Options:

• Download the book as pdf (12 MB)
• Download the additional web material as pdf (1.3 MB)
• Download individual chapters from the list of contents below

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

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).

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.