biostudies-literatureJabado OJNEI NIH HHSNIAID NIH HHSNHLBI NIH HHSNIGMS NIH HHS354https://www.ebi.ac.uk/biostudies/studies/S-EPMC2909221biostudies-literatureUnknown11<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.BMC bioinformaticsNonparametric methods for the analysis of single-color pathogen microarrays.PMC2909221R01 HL083850T32GM008224EY017404AI57158-05U54 AI057158R24 EY017404AI070411U01 AI070411HL083850Quan PLLipkin WIBriese THui JJabado OJConlan SHornig MPalacios GfalseNonparametric methods for the analysis of single-color pathogen microarrays.<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.2010-01-01T00:00:00Z2010 Jun2024-10-15T02:34:38.979Z2019-03-27T00:32:40ZS-EPMC29092212058433110.1186/1471-2105-11-354