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→Microarray Analysis
==Microarray Analysis==
*set up design matrix. Use a different integer for each treatment group. The following example is for a contrast between the first four seven groups and the last four eight groups. For details on other design matrices see chapter 8 of [[http://www.bioconductor.org/packages/2.3/bioc/vignettes/limma/inst/doc/usersguide.pdf limma User Guide]]
<pre>
pData(eset) #to see phenotype annotation data
design <- model.matrix(~(c(1,1,1,1,1,1,1,0,0,0,0,10,10,10,10)),eset) #for four replicates of each treatment group,
colnames(design) <- c("resistant","sensitive") # give names to the treatment groups
design #check the design matrix
</pre>
