analysing time course microarray data using bioconductor a case study using yeast2 affymetrix arrays分析时间进程使用bioconductor案例研究使用微阵列数据yeast2 affymetrix数组.pdfVIP

Gillespie et al. BMC Research Notes 2010, 3:81 /1756-0500/3/81 S HO RT REPORT Open Access Short Report Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays Colin S Gillespie*†1,2, Guiyuan Lei†1,2, Richard J Boys1,2, Amanda Greenall2,3 and Darren J Wilkinson 1,2 Abstract Background: 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. Findings: 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 http://www.mas.ncl.ac.uk/ ~ncsg3/microarray/. Conclusions: CRAN and Bioconductor are stable repositories that provide a wide variety of appropriate statistical tools to analyse time course microarray data. Introduction throughout the analysis we give the R commands that pro- As experimental costs decrease, large scale microarray duce the numerical/graphical output shown in this paper. A experiments are becoming increasingly routine, particularly maintained version of the R commands can be found at those which track a number of different cell