Comprehensive Quality Control Utilizing the Prehybridization Third-dye Image Leads to Accurate Gene Expression Measurements by CDNA Microarrays

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2006 Aug 16

PMID 16907976

Citations 4

Authors

Xujing Wang

Shuang Jia

Lisa Meyer

Bixia Xiang

Li-Yen Chen

Nan Jiang

Carol Moreno

Howard J Jacob

Soumitra Ghosh

Martin J Hessner

Affiliations

Soon will be listed here.

Abstract

Background: Gene expression profiling using microarrays has become an important genetic tool. Spotted arrays prepared in academic labs have the advantage of low cost and high design and content flexibility, but are often limited by their susceptibility to quality control (QC) issues. Previously, we have reported a novel 3-color microarray technology that enabled array fabrication QC. In this report we further investigated its advantage in spot-level data QC.

Results: We found that inadequate amount of bound probes available for hybridization led to significant, gene-specific compression in ratio measurements, increased data variability, and printing pin dependent heterogeneities. The impact of such problems can be captured through the definition of quality scores, and efficiently controlled through quality-dependent filtering and normalization. We compared gene expression measurements derived using our data processing pipeline with the known input ratios of spiked in control clones, and with the measurements by quantitative real time RT-PCR. In each case, highly linear relationships (R2 > 0.94) were observed, with modest compression in the microarray measurements (correction factor < 1.17).

Conclusion: Our microarray analytical and technical advancements enabled a better dissection of the sources of data variability and hence a more efficient QC. With that highly accurate gene expression measurements can be achieved using the cDNA microarray technology.

Citing Articles

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Multiplexed method to calibrate and quantitate fluorescence signal for allergen-specific IgE.

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Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling.

Gao S, Hartman 4th J, Carter J, Hessner M, Wang X BMC Syst Biol. 2010; 4:167.

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Quality Weighted Mean and T-test in Microarray Analysis Lead to Improved Accuracy in Gene Expression Measurements and Reduced Type I and II Errors in Differential Expression Detection.

Gao S, Jia S, Hessner M, Wang X J Comput Sci Syst Biol. 2010; 1:41.

PMID: 20151041 PMC: 2819534. DOI: 10.4172/jcsb.1000003.

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