A revised design for microarray experiments to account for experimental noise and uncertainty of probe response

PloS One
Alex E PozhitkovDiethard Tautz

Abstract

Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal re...Continue Reading

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Citations

Mar 23, 2017·Forensic Science International : Synergy·M Colby HunterPeter A Noble
Jan 27, 2017·Open Biology·Alex E PozhitkovPeter A Noble
Aug 8, 2018·Journal of Biomolecular Structure & Dynamics·Y V StirmanovY D Nechipurenko
Sep 19, 2017·Communicative & Integrative Biology·Alexander E Pozhitkov, Peter A Noble
Sep 16, 2018·BMC Genomics·Peter A Noble, Alexander E Pozhitkov
Aug 9, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Alexander E Pozhitkov, Peter A Noble

Related Concepts

Calibration
Cdna Microarrays
MRNA Differential Display
DNA Copy Number Changes
Biomedical Research
Experimental Design
Gene Expression
Probes
Evaluation
Research Study

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