Using Bioconductor To Analyse Microarray Data: Difference between revisions
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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. | *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 | |||