A proposed metric for assessing the measurement quality of individual microarrays

Kyoungmi Kim, Grier P. Page, T. Mark Beasley, Stephen Barnes, Katherine E. Scheirer, David B. Allison

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Background: High-density microarray technology is increasingly applied to study gene expression levels on a large scale. Microarray experiments rely on several critical steps that may introduce error and uncertainty in analyses. These steps include mRNA sample extraction, amplification and labeling, hybridization, and scanning. In some cases this may be manifested as systematic spatial variation on the surface of microarray in which expression measurements within an individual array may vary as a function of geographic position on the array surface. Results: We hypothesized that an index of the degree of spatiality of gene expression measurements associated with their physical geographic locations on an array could indicate the summary of the physical reliability of the microarray. We introduced a novel way to formulate this index using a statistical analysis tool. Our approach regressed gene expression intensity measurements on a polynomial response surface of the microarray's Cartesian coordinates. We demonstrated this method using a fixed model and presented results from real and simulated datasets. Conclusion: We demonstrated the potential of such a quantitative metric for assessing the reliability of individual arrays. Moreover, we showed that this procedure can be incorporated into laboratory practice as a means to set quality control specifications and as a tool to determine whether an array has sufficient quality to be retained in terms of spatial correlation of gene expression measurements.

Original languageEnglish (US)
Article number35
JournalBMC Bioinformatics
Volume7
DOIs
StatePublished - Jan 23 2006
Externally publishedYes

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Microarrays
Microarray
Gene expression
Gene Expression
Metric
Geographic Locations
Quality Control
Uncertainty
Response Surface
Spatial Correlation
Cartesian
Amplification
Messenger RNA
Labeling
Statistical Analysis
Quality control
Scanning
Technology
Statistical methods
Polynomials

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Kim, K., Page, G. P., Beasley, T. M., Barnes, S., Scheirer, K. E., & Allison, D. B. (2006). A proposed metric for assessing the measurement quality of individual microarrays. BMC Bioinformatics, 7, [35]. https://doi.org/10.1186/1471-2105-7-35

A proposed metric for assessing the measurement quality of individual microarrays. / Kim, Kyoungmi; Page, Grier P.; Beasley, T. Mark; Barnes, Stephen; Scheirer, Katherine E.; Allison, David B.

In: BMC Bioinformatics, Vol. 7, 35, 23.01.2006.

Research output: Contribution to journalArticle

Kim, Kyoungmi ; Page, Grier P. ; Beasley, T. Mark ; Barnes, Stephen ; Scheirer, Katherine E. ; Allison, David B. / A proposed metric for assessing the measurement quality of individual microarrays. In: BMC Bioinformatics. 2006 ; Vol. 7.
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