Microarry Gene Expression Data Analysis

Bibliographic Details
Main Author: Helen C Causton
Other Authors: John Quackenbush; Alvis Brazma
Format: Printed Book
Published: Malden, MA Blackwell 2003
Subjects:
DNA microarrays. Gene expression > Research > Methodology. Oligonucleotide Array Sequence Analysis > methods.
Table of Contents:
  • The central dogma of molecular biology
  • What are microarrays and how do they work?
  • Gene function and drug discovery
  • Data generation, processing and analysis: an overview
  • Data management
  • Experimental design
  • Experimental objectives and features of microarray data
  • General principles of experimental design
  • Reducing the number of variables
  • Time courses vs. independent data points
  • Replicates and repeated measurements
  • Reference samples
  • Exogenous ('spiked-in') controls
  • Dual labelling/dye swapping
  • Validation of results
  • Choice and preparation of samples
  • Obtaining the appropriate sample
  • Strain background
  • Mutants
  • Reagents
  • Sample and sample composition
  • Small amounts of sample: RNA amplification and pooling
  • Preparation of the labelled extract
  • Assessing the quality of the labelled extract
  • Choice and design of arrays
  • Choice of array platform
  • Oligonucleotides vs. PCR products
  • Replicate, guide and control features
  • Cross-hybridisation
  • Hybridisation, scanning and quality control
  • Long-term considerations
  • Record keeping
  • Standardisation
  • Image processing, normalisation and data transformation
  • Preliminary processing of the data
  • Image analysis
  • Measuring and reporting expression
  • Saturated pixels
  • The appropriate number of pixels
  • Estimating background
  • Reporting expression with Affymetrix GeneChips
  • Expression ratios: the starting point for sample comparison
  • Transformations of the expression ratio.

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