Nonparametric methods for the analysis of single-color pathogen microarrays

Omar J. Jabado, Sean Conlan, Phenix Lan Quan, Jeffrey Hui, Gustavo Palacios, Mady Hornig, Thomas Briese, W. Ian Lipkin

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied.Results: Positive predictive value and false positive rates were examined to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, the chi-square proved most useful.Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.

Original languageEnglish
Article number354
JournalBMC Bioinformatics
Volume11
DOIs
StatePublished - 28 Jun 2010
Externally publishedYes

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