Microarray Experiments: A Conceptual View and Practical Considerations

View Part One

Goals for the multimedia presentation include:

• Discuss experimental design and its importance in obtaining the biological relevance from your data
• Demonstrate the utility of the GeneChip® expression assay in biomedical research that goes beyond target discovery
• Illustrate the path from a specific biological question, through experimental design and data analysis, and into biological interpretation
• Tell a biological story: how Retinoic Acid drives neutrophil precursors to stop dividing and complete their maturation

Content includes a discussion on the basics of experimental design, sources of experimental variability, controlling technical variability, controlling biological variability, experimental replicates, the use of coefficient of variation to determine the appropriate number of experimental replicates, and the application of these topics through the discussion of an example experiment (Investigating Neutrophil Maturation: An Approach to Experimental Design and Data Analysis).

The content of Microarray Experiments: A Conceptual View and Practical Considerations is most appropriate for beginning level GeneChip® microarray users. This talk and multimedia presentation provides valuable information and insights from experienced Affymetrix scientists.

Microarray Experiments: Coming to Grips with the PLIER Algorithm

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Goals for the multimedia presentation include:

• To introduce the PLIER algorithm for calculating Signal Intensities for expression arrays

Part two of the Expression Data Analysis four part series includes a high-level overview of the algorithm, approach, and benefits. The presentation begins with general information on measurement, moves to specifics about the PLIER algorithm and algorithm performance, and concludes with information on PLIER algorithm availability.

Microarray Experiments: Statistical Tools and Data Visualization

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Goals for the multimedia presentation include:

• High-level overview of available tools
• How to filter data and prioritize transcropts for further study
• How to classify and distinguish samples based on differences in their Expression Profile

Part three of the Expression Data Analysis four part series includes an overview of methods to find transcripts of interest, a discussion of how to combine statistical tests with robust experimental design, an overview of how to use clustering to identify similar samples or transcripts with related expression patterns, and the use of classification techniques to identify gene expression signatures correlated with other parameters.

Microarray Experiments: Biological Interpretation of Microarray Data

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Goals for the multimedia presentation include:

• Overview of a data analysis workflow and the biological interpretation of data
• Approach for placing expression data into a functional context

Part four of the Expression Data Analysis four part series includes a review of the data analysis workflow, a discussion of gene annotation enhancements and the tools to systematically organize them, allowing for data mining and interpretation on a functional level, a comparison of statistical and biological significance, a review of information available in the NetAffx™ Analysis Center, a demonstration of how to create gene ontology (GO) graphs, a review of methods for filtering gene lists, a demonstration of how to visualize probe sets in the genome context using the Integrated Genome Browser, and a discussion of pathway analysis tools.

Related Content

• Software Products
• Reagents & Assays
• GeneChip® Expression Analysis Technical Manual
• Affymetrix Microarray Bulletin