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DNA Microarrays

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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Updated: Jun 3, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

A wholly defined Agilent microarray spike-in dataset.

Qianqian Zhu¹, Jeffrey C Miecznikowski, Marc S Halfon

¹Department of Biochemistry, Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214, USA. qzhu@buffalo.edu

Bioinformatics (Oxford, England)

|March 19, 2011

Summary

This summary is machine-generated.

A new Agilent microarray spike-in dataset, "Ag Spike," enables direct comparison with Affymetrix platforms. This resource aids in evaluating two-color array analysis methods and shows high agreement between platforms.

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Area of Science:

Genomics
Bioinformatics
Microarray Technology

Background:

Spike-in datasets are crucial for evaluating microarray analysis strategies.
Previous datasets like Golden and Platinum Spikes informed Affymetrix GeneChip analysis.
A defined spike-in dataset for two-color platforms was previously unavailable.

Purpose of the Study:

To generate a wholly defined spike-in dataset for Agilent microarrays.
To facilitate direct cross-platform comparisons between Agilent and Affymetrix platforms.
To evaluate analysis methods for two-color microarrays.

Main Methods:

Generation of the 'Ag Spike' dataset comprising 12 arrays.
Inclusion of over 2000 differentially expressed and 3600 background cRNAs.
Ensuring identical composition to the Platinum Spike dataset for cross-platform analysis.

Main Results:

The 'Ag Spike' dataset is now available for Agilent microarrays.
Demonstrated utility of the dataset for evaluating two-color array analysis methods.
High agreement observed between Agilent (Ag Spike) and Affymetrix (Platinum Spike) platforms.

Conclusions:

The 'Ag Spike' dataset is a valuable resource for the scientific community.
Enables robust evaluation and comparison of microarray analysis techniques.
Confirms high concordance between major microarray platforms.