Microarray

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Time Course

http://www.biostat.jhsph.edu/~ririzarr/688/

Limma package

http://master.bioconductor.org/help/course-materials/2005/BioC2005/labs/lab01/drosEmbryo/ (note the package drosEmbryo is not available on Bioc)
http://bioinf.wehi.edu.au/marray/jsm2005/lab5/lab5.html

A case study using Limma package

http://www.biomedcentral.com/1756-0500/3/81

timecourse package

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