Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007;8(9):R190.
doi: 10.1186/gb-2007-8-9-r190.

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data

Michael Watson  1 , Juliet Dukes, Abu-Bakr Abu-Median, Donald P King, Paul Britton
Affiliations

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data

Michael Watson et al. Genome Biol. 2007.

Abstract

DNA microarrays offer the possibility of testing for the presence of thousands of micro-organisms in a single experiment. However, there is a lack of reliable bioinformatics tools for the analysis of such data. We have developed DetectiV, a package for the statistical software R. DetectiV offers powerful yet simple visualization, normalization and significance testing tools. We show that DetectiV performs better than previously published software on a large, publicly available dataset.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Flow of information, and steps taken, when analyzing pathogen detection microarray data using DetectiV.
Figure 2
Figure 2
GSM40814 by family. Example barplot from DetectiV showing data from a virus detection microarray. The sample included amplified RNA from nasal lavage, positive for respiratory syncytial virus by DFA. Oligos have been averaged over replicates and grouped according to virus family. Each unique oligo is represented by a single bar. Each virus family has a unique background color. The y-axis is raw intensity.
Figure 3
Figure 3
GSM40814 Paramyxoviridae by species. Example barplot from DetectiV showing data from a virus detection microarray. The sample included amplified RNA from nasal lavage, positive for respiratory syncytial virus by DFA. Only oligos representing species from the Paramyxoviridae family are shown. Oligos have been averaged over replicates and grouped according to virus species. Each unique oligo is represented by a single bar. Each virus species has a unique background color. The y-axis is raw intensity.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Lapa S, Mikheev M, Shchelkunov S, Mikhailovich V, Sobolev A, Blinov V, Babkin I, Guskov A, Sokunova E, Zasedatelev A, et al. Species-level identification of orthopoxviruses with an oligonucleotide microchip. J Clin Microbiol. 2002;40:753–757. doi: 10.1128/JCM.40.3.753-757.2002. - DOI - PMC - PubMed
    1. Boonham N, Walsh K, Smith P, Madagan K, Graham I, Barker I. Detection of potato viruses using microarray technology: towards a generic method for plant viral disease diagnosis. J Virol Methods. 2003;108:181–187. doi: 10.1016/S0166-0934(02)00284-7. - DOI - PubMed
    1. Song Y, Dai E, Wang J, Liu H, Zhai J, Chen C, Du Z, Guo Z, Yang R. Genotyping of hepatitis B virus HBV by oligonucleotides microarray. Mol Cell Probes. 2006;20:121–127. doi: 10.1016/j.mcp.2005.11.004. - DOI - PubMed
    1. Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, et al. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003;1:E2. doi: 10.1371/journal.pbio.0000002. - DOI - PMC - PubMed
    1. Perrin A, Duracher D, Perret M, Cleuziat P, Mandrand B. A combined oligonucleotide and protein microarray for the codetection of nucleic acids and antibodies associated with human immunodeficiency virus, hepatitis B virus, and hepatitis C virus infections. Anal Biochem. 2003;322:148–155. doi: 10.1016/j.ab.2003.08.002. - DOI - PubMed

Publication types