Nonparametric methods for the analysis of single-color pathogen microarrays

BMC Bioinformatics

Methodology Article

Sean Conlan¹  Phenix-Lan Quan¹  Gustavo Palacios¹  Mady Hornig¹  Thomas Briese¹  Jeffrey Hui¹  Omar J Jabado¹  W Ian Lipkin¹ 

[1] Center for Infection and Immunity Mailman School of Public Health, Columbia University, New York, NY, USA;

关键词: Positive Predictive Value;    Respiratory Syncytial Virus;    False Positive Rate;    West Nile Virus;    Binomial Test;   

DOI  :  10.1186/1471-2105-11-354

 received in 2009-07-24, accepted in 2010-06-28,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsPositive 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Jabado et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.