Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays

• Main Authors: Boys Richard J, Lei Guiyuan, Gillespie Colin S, Greenall Amanda, Wilkinson Darren J
• Format: Article
• Language: English
• Published: BMC 2010-03-01
• Series: BMC Research Notes
• Online Access: http://www.biomedcentral.com/1756-0500/3/81

<p>Abstract</p> <p>Background</p> <p>Large scale microarray experiments are becoming increasingly routine, particularly those which track a number of different cell lines through time. This time-course information provides valuable insight into the dynamic mechanisms underlying the biological processes being observed. However, proper statistical analysis of time-course data requires the use of more sophisticated tools and complex statistical models.</p> <p>Findings</p> <p>Using the open source CRAN and Bioconductor repositories for R, we provide example analysis and protocol which illustrate a variety of methods that can be used to analyse time-course microarray data. In particular, we highlight how to construct appropriate contrasts to detect differentially expressed genes and how to generate plausible pathways from the data. A maintained version of the R commands can be found at <url>http://www.mas.ncl.ac.uk/~ncsg3/microarray/</url>.</p> <p>Conclusions</p> <p>CRAN and Bioconductor are stable repositories that provide a wide variety of appropriate statistical tools to analyse time course microarray data.</p>