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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Consolidated strategy for the analysis of microarray spike-in data.

Matthew N McCall1, Rafael A Irizarry

  • 1Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA.

Nucleic Acids Research
|August 5, 2008
PubMed
Summary

New spike-in experiments and statistical methods enable standardized microarray platform comparisons. This addresses confusion in selecting optimal platforms, protocols, and analysis tools for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microarray Technology

Background:

  • Microarray technology is increasingly used, necessitating reliable platform assessments and comparisons.
  • Existing statistical assessments of microarray data are inconsistent and lack cross-platform comparability, causing confusion.
  • Current methods hinder objective selection of optimal platforms, protocols, and analysis tools.

Purpose of the Study:

  • To introduce novel spike-in experiments for microarray analysis.
  • To present a new statistical solution for enabling cross-platform comparisons.
  • To propose a comprehensive procedure for microarray platform assessments.

Main Methods:

  • Development of two new spike-in experiments.
  • Introduction of a novel statistical method for cross-platform comparability.
  • Implementation of a user-friendly Bioconductor package (spkTools).

Main Results:

  • Demonstrated the first spike-in-based comparison of Affymetrix, Agilent, and Illumina platforms.
  • Provided a standardized framework for microarray platform assessment.
  • Enabled objective comparison of different microarray technologies.

Conclusions:

  • The developed spkTools package and methodology facilitate robust, cross-platform microarray comparisons.
  • This work clarifies best practices for selecting microarray platforms, protocols, and analysis tools.
  • Standardized assessments are crucial for advancing microarray technology utilization.