Protocols for the assurance of microarray data quality and process control

L. D. Burgoon, Jeanette E Eckel-Passow, C. Gennings, D. R. Boverhof, J. W. Burt, C. J. Fong, T. R. Zacharewski

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Microarrays represent a powerful technology that provides the ability to simultaneously measure the expression of thousands of genes. However, it is a multi-step process with numerous potential sources of variation that can compromise data analysis and interpretation if left uncontrolled, necessitating the development of quality control protocols to ensure assay consistency and high-quality data. In response to emerging standards, such as the minimum information about a microarray experiment standard, tools are required to ascertain the quality and reproducibility of results within and across studies. To this end, an intralaboratory quality control protocol for two color, spotted microarrays was developed using cDNA microarrays from in vivo and n vitro dose-response and time-course studies. The protocol combines: (i) diagnostic plots monitoring the degree of feature saturation, global feature and background intensities, and feature misalignments with (ii) plots monitoring the intensity distributions within arrays with (iii) a support vector machine (SVM) model. The protocol is applicable to any laboratory with sufficient datasets to establish historical high- and low-quality data.

Original languageEnglish (US)
Pages (from-to)1-11
Number of pages11
JournalNucleic Acids Research
Volume33
Issue number19
DOIs
StatePublished - 2005

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Quality Control
Aptitude
Oligonucleotide Array Sequence Analysis
Reproducibility of Results
Reaction Time
Color
Technology
Gene Expression
Data Accuracy
Support Vector Machine
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

Burgoon, L. D., Eckel-Passow, J. E., Gennings, C., Boverhof, D. R., Burt, J. W., Fong, C. J., & Zacharewski, T. R. (2005). Protocols for the assurance of microarray data quality and process control. Nucleic Acids Research, 33(19), 1-11. https://doi.org/10.1093/nar/gni167

Protocols for the assurance of microarray data quality and process control. / Burgoon, L. D.; Eckel-Passow, Jeanette E; Gennings, C.; Boverhof, D. R.; Burt, J. W.; Fong, C. J.; Zacharewski, T. R.

In: Nucleic Acids Research, Vol. 33, No. 19, 2005, p. 1-11.

Research output: Contribution to journalArticle

Burgoon, LD, Eckel-Passow, JE, Gennings, C, Boverhof, DR, Burt, JW, Fong, CJ & Zacharewski, TR 2005, 'Protocols for the assurance of microarray data quality and process control', Nucleic Acids Research, vol. 33, no. 19, pp. 1-11. https://doi.org/10.1093/nar/gni167
Burgoon, L. D. ; Eckel-Passow, Jeanette E ; Gennings, C. ; Boverhof, D. R. ; Burt, J. W. ; Fong, C. J. ; Zacharewski, T. R. / Protocols for the assurance of microarray data quality and process control. In: Nucleic Acids Research. 2005 ; Vol. 33, No. 19. pp. 1-11.
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