Sources of nonlinearity in cDNA microarray expression measurements.

L. Ramdas, K. R. Coombes, K. Baggerly, L. Abruzzo, W Edward Jr. Highsmith, T. Krogmann, S. R. Hamilton, W. Zhang

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

BACKGROUND: A key assumption in the analysis of microarray data is that the quantified signal intensities are linearly related to the expression levels of the corresponding genes. To test this assumption, we experimentally examined the relationship between signal and expression for the two types of microarrays we most commonly encounter: radioactively labeled cDNAs on nylon membranes and fluorescently labeled cDNAs on glass slides. RESULTS: We uncovered two sources of nonlinearity. The first, which led to discrepancies in analysis affecting the fluorescent signals, was signal quenching associated with excessive dye concentrations. The second, affecting the radioactive signals, was a nonlinear transformation of the raw data introduced by the scanner. Correction for this transformation was made by some, but not all, image-quantification software packages. CONCLUSIONS: The second type of nonlinearity is more troublesome, because it could not have been predicted a priori. Both types of nonlinearities were detected by simple dilution series, which we recommend as a quality-control step.

Original languageEnglish (US)
JournalGenome Biology
Volume2
Issue number11
StatePublished - 2001
Externally publishedYes

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scanners
nylon
Oligonucleotide Array Sequence Analysis
nonlinearity
quality control
dyes
glass
Complementary DNA
Nylons
Microarray Analysis
Quality Control
Glass
Coloring Agents
Software
genes
testing
Membranes
Genes
scanner
dye

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Ramdas, L., Coombes, K. R., Baggerly, K., Abruzzo, L., Highsmith, W. E. J., Krogmann, T., ... Zhang, W. (2001). Sources of nonlinearity in cDNA microarray expression measurements. Genome Biology, 2(11).

Sources of nonlinearity in cDNA microarray expression measurements. / Ramdas, L.; Coombes, K. R.; Baggerly, K.; Abruzzo, L.; Highsmith, W Edward Jr.; Krogmann, T.; Hamilton, S. R.; Zhang, W.

In: Genome Biology, Vol. 2, No. 11, 2001.

Research output: Contribution to journalArticle

Ramdas, L, Coombes, KR, Baggerly, K, Abruzzo, L, Highsmith, WEJ, Krogmann, T, Hamilton, SR & Zhang, W 2001, 'Sources of nonlinearity in cDNA microarray expression measurements.', Genome Biology, vol. 2, no. 11.
Ramdas L, Coombes KR, Baggerly K, Abruzzo L, Highsmith WEJ, Krogmann T et al. Sources of nonlinearity in cDNA microarray expression measurements. Genome Biology. 2001;2(11).
Ramdas, L. ; Coombes, K. R. ; Baggerly, K. ; Abruzzo, L. ; Highsmith, W Edward Jr. ; Krogmann, T. ; Hamilton, S. R. ; Zhang, W. / Sources of nonlinearity in cDNA microarray expression measurements. In: Genome Biology. 2001 ; Vol. 2, No. 11.
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