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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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Related Experiment Video

Updated: Mar 15, 2026

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs

Published on: April 14, 2015

Assessing Agreement between miRNA Microarray Platforms.

Niccolò P Bassani¹, Federico Ambrogi², Elia M Biganzoli¹

¹Department of Clinical Sciences and Community Health, University of Milan, Via Vanzetti 5 20133, Milano (MI), Italy.

Microarrays (Basel, Switzerland)

|September 8, 2016

Summary

This summary is machine-generated.

This study introduces a modified Bland-Altman plot to evaluate agreement between miRNA microarray platforms. The method revealed good concordance for Agilent and Illumina, but poor-to-moderate agreement for Affymetrix.

Keywords:

Bland–Altman agreement measurement error miRNA microarray reliability

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Last Updated: Mar 15, 2026

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Published on: August 21, 2019

Area of Science:

Biotechnology
Genomics
Medical Diagnostics

Background:

MicroRNA (miRNA) microarrays are crucial for understanding disease mechanisms.
Limited studies assess concordance between miRNA microarray platforms considering measurement error.

Purpose of the Study:

To propose and validate a modified Bland-Altman plot for assessing agreement between miRNA microarray platforms.
To evaluate the concordance of Affymetrix, Agilent, and Illumina miRNA platforms.

Main Methods:

Profiling of a renal tumor cell line and normal human tissues on three miRNA platforms (Affymetrix, Agilent, Illumina) in triplicate.
Assessment of intra-platform reliability using concordance correlation coefficients (CCC and OCCC).
Application of a modified Bland-Altman plot to analyze inter-platform agreement, accounting for measurement error and bias.

Main Results:

All platforms demonstrated moderate-to-good intra-platform repeatability (CCC and OCCC).
Modified Bland-Altman analysis showed good concordance for Agilent and Illumina platforms.
Affymetrix platform exhibited poor-to-moderate agreement between samples.

Conclusions:

The modified Bland-Altman plot effectively assesses agreement between miRNA microarray platforms, accounting for measurement error.
Agilent and Illumina platforms show better concordance compared to Affymetrix for miRNA profiling.
The method is adaptable for evaluating concordance across various array-based technologies.