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*see [[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/geo/ Peter Cock's Page]] or [[http://www.bioconductor.org/packages/1.8/bioc/html/GEOquery.html GEOquery Documentation]] for more information.
==Microarray Analysis==
*set up design matrix. Use a different integer for each treatment group.
<pre>
pData(eset) #to see phenotype annotation data
design <- model.matrix(~0+factor(c(1,1,1,1,2,2,2,2)),eset) #for four replicates of each treatment group
colnames(design) <- c("resistant","sensitive") # give names to the treatment groups
