Gene Expression Studies Using Affymetrix Microarrays

The Affymetrix GeneChip® system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of experience in practical expression profiling experiments and data analyses, Gene Expression Studies Using Affymetrix Microarrays tears down the omnipresent language barriers among molecular biology, bioinformatics, and biostatistics by explaining the entire process of a gene expression study from conception to conclusion.

Truly Multidisciplinary: Merges Molecular Biology, Bioinformatics, and Biostatistics
This authoritative resource covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative, full-color examples, enabling those inexperienced with gene expression studies to grasp the basic principles.
Gene Expression Studies Using Affymetrix Microarrays provides novices with a detailed, yet focused introductory course and practical user guide. Specialized experts will also find it useful as a translation dictionary to understand other involved disciplines or to get a broader picture of microarray gene expression studies in general. Although focusing on Affymetrix gene expression, this globally relevant guide covers topics that are equally useful for other microarray platforms and other Affymetrix applications.

Hinrich Göhlmann and Willem Talloen work at Johnson & Johnson Pharmaceutical R&D as Principal Scientist and Senior Biostatistician, respectively.

Biological question
Why gene expression?
Biotechnological advancements
Research Question
Main types of research questions
Affymetrix microarrays
Probes
Probe sets
Array types
Standard lab processes
Affymetrix data quality
Running the experiment
Biological experiment
Microarray experiment
Data analysis preparation
Data preprocessing
Quality control
Data analysis
Why do we need statistics?
The curse of high-dimensionality
Gene filtering
Unsupervised data exploration
Detecting differential expression
Supervised prediction
Pathway analysis
Other analysis approaches
Presentation of results
Data visualization
Biological Interpretation
Data publishing
Reproducible research
Pharmaceutical R&D
The need for early indications
Critical Path Initiative
Drug Discovery
Drug Development
Clinical Trials
Using R and Bioconductor
R and Bioconductor
R and Sweave
R and Eclipse
Automated array analysis
Other software for microarray analysis
Future Perspectives
Co-analyzing different data types
The microarrays of the future
Next-gen sequencing: The end for microarrays?
Bibliography