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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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An adaptive single-step FDR procedure with applications to DNA microarray analysis.

Vishwanath Iyer¹, Sanat Sarkar

¹Bristol Myers Squibb Pharm. Inc, 5 Research Parkway, Wallingford, CT 06492, USA. viyer@temple.edu

Biometrical Journal. Biometrische Zeitschrift

|March 9, 2007

Summary

This study enhances False Discovery Rate (FDR) control in DNA microarray analysis by modifying a single-step procedure. The adaptive method improves FDR control, offering better insights for exploratory research.

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Last Updated: Jul 16, 2026

A Droplet-Based Microfluidic Approach and Microsphere-PCR Amplification for Single-Stranded DNA Amplicons

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Published on: November 14, 2018

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

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High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries

High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries

Published on: August 12, 2019

Area of Science:

Statistics
Bioinformatics
Genomics

Background:

Multiple hypothesis testing is crucial in DNA microarray analysis.
Traditional FWER procedures are inadequate for exploratory research.
False Discovery Rate (FDR) control is preferred for managing false positives.

Purpose of the Study:

To modify the Genovese-Wasserman single-step FDR procedure for improved control.
To develop an adaptive FDR procedure using mixture model estimation.
To evaluate the performance of the proposed adaptive procedure.

Main Methods:

Modification of the Genovese-Wasserman procedure for FDR control.
Estimation of mixture of two normals parameters using the EM algorithm.
Numerical verification of the adaptive procedure's properties.

Main Results:

The modified procedure demonstrates improved FDR control closer to the target level alpha.
The adaptive procedure, utilizing estimated parameters, shows effective FDR control.
Numerical comparisons validate the performance against existing methods.

Conclusions:

The proposed adaptive FDR procedure offers enhanced control for DNA microarray analysis.
This method is particularly beneficial for exploratory studies.
The adaptive approach provides a robust alternative to existing FDR controlling procedures.