DetectiV: Analysis of pathogen detection microarray data


One of the key applications of metagenomics is the identification and quantification of species within a clinical or environmental sample. DNA microarrays offer a practical and affordable method of testing for the presence of thousands of species in a single experiment, an attractive alternative to cloning and sequencing. Many microarrays have already been produced with the aim of characterising the population of microorganisms present in a sample, incluiding detection of known viruses, assessment of bioterrorism and monitoring food quality.

We present DetectiV, a package for R containing functions for visualisation, normalisation and significance testing of pathogen detection microarray data. R is a freely available statistical software packages available for Windows, Unix/Linux and MacOS, meaning DetectiV is a platform independent solution. DetectiV uses simple and established methods for visualisation, normalisation and significance testing. When applied to a publicly available microarray dataset, DetectiV produces the correct result in 55 out of 56 arrays tested, an improvement on previously published methods.


DetectiV is available to download from sourceforge


DetectiV is a package for R, an amazingly powerful open-source statistical environment. R is available for windows, linux or Mac OSX.

After installing R, Windows users should download the latest DetectiV .zip file, and install using the menu bar:

	Packages -> Install package(s) from local zip files...

Linux users should download the latest .tar.gz file and, after installing R, type:

	R CMD INSTALL DetectiV_%.%.tar.gz

(where %.% is the version of the file you have downloaded.


A tutorial for the DetectiV package can be found here

Supporting Data

Full results of the analysis of the Urisman et al dataset can be found here: here
Full results of the analysis of the IAH/VLA dataset can be found here: here


Michael Watson
Informatics Group
Institute for Animal Health
Compton Laboratory
RG20 7NN