DetectiV: Analysis of pathogen detection microarray data

Introduction

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.