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Exercises:DNA microarray analysis

We will use the TIGR MultiExperiment Viewer (TMEV) Java software package for the analysis of microarray data. You will look at the distribution of measured microarray fluorescence intensities and see the influence of normalization. Furthermore, you will apply some unsupervised learning techniques such as hierarchical clustering, self-organizing maps, and k-means clustering on simulated microarray data. You will also apply hierarchical clustering on a yeast cell-cycle microarray data set as published by Spellman et al.

  • Microarray software: The exercises use the TIGR Multiexperiment Viewer (TMEV) Java software package. TMEV is installed on the PCs in the exercise rooms. If you want to work on the exercises elsewhere, here is what is needed:
    • TIGR Multiple Experiment Viewer (zip file of version 3.1) Just unzip it and click on TMEV.bat to start the program. Note that, TMEV v3.1 runs on the Windows, Mac OSX or Linux operating systems and requires Java v1.4.1 or higher. Java 3D is also required for some MeV modules, like PCA.
    • Download Java v1.4.2 (download the J2SE JRE)
    • Download Java 3D v1.5.1
Topic revision: r8 - 2013-03-07 - PerryMoerland
 
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