Using Bioconductor To Analyse Microarray Data: Difference between revisions
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==Microarray Analysis== | ==Microarray Analysis== | ||
*set up design matrix. Use a different integer for each treatment group. | *set up design matrix. Use a different integer for each treatment group. The following example is for a contrast between the first four groups and the last four 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> | <pre> | ||
pData(eset) #to see phenotype annotation data | pData(eset) #to see phenotype annotation data | ||
design <- model.matrix(~ | design <- model.matrix(~(c(0,0,0,0,1,1,1,1)),eset) #for four replicates of each treatment group, | ||
colnames(design) <- c("resistant","sensitive") # give names to the treatment groups | colnames(design) <- c("resistant","sensitive") # give names to the treatment groups | ||
design #check the design matrix | design #check the design matrix | ||
</pre> | </pre> | ||