title: Nonparametric methods for the analysis of single-color pathogen microarrays.
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.
authors.affiliation: Center for Infection and Immunity Mailman School of Public Health Columbia University New York, NY, USA.
authors.forename: Omar J
authors.initials: OJ
authors.lastname: Jabado
authors.forename: Sean
authors.initials: S
authors.lastname: Conlan
authors.forename: Phenix-Lan
authors.initials: PL
authors.lastname: Quan
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Hui
authors.forename: Gustavo
authors.initials: G
authors.lastname: Palacios
authors.forename: Mady
authors.initials: M
authors.lastname: Hornig
authors.forename: Thomas
authors.initials: T
authors.lastname: Briese
authors.forename: W Ian
authors.initials: WI
authors.lastname: Lipkin
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D006801:Humans; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012015:Reference Standards; D014780:Viruses / Q000235:genetics*