Unknown,Transcriptomics,Genomics,Proteomics

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Viral Microarray - Cultured Virus Set


ABSTRACT: Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays 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: An examination of both positive predictive value and false positive rates was employed 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, it was the chi-square that 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. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.

ORGANISM(S): Influenza A virus (A/Texas/36/1991(H1N1))

SUBMITTER: Omar Jabado 

PROVIDER: E-GEOD-21318 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Nonparametric methods for the analysis of single-color pathogen microarrays.

Jabado Omar J OJ   Conlan Sean S   Quan Phenix-Lan PL   Hui Jeffrey J   Palacios Gustavo G   Hornig Mady M   Briese Thomas T   Lipkin W Ian WI  

BMC bioinformatics 20100628


<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 f  ...[more]

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