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Using Bioconductor To Analyse Microarray Data

204 bytes added, 01:16, 27 July 2009
m
→‎Microarray Analysis
<pre>
library(limma) #load limma package
library(affyPLM) #load affyPLM package
eset.norm <- normalize.ExpressionSet.quantiles(eset) #normalize expression set by quantile method
pData(eset) #to see phenotype annotation data
design <- model.matrix(~(c(1,1,1,1,1,1,1,0,0,0,0,0,0,0,0)),eset) #set design matirx
colnames(design) <- c("resistant","sensitive") # give names to the treatment groups
design #check the design matrix
fit <- lmFit(eset.norm,design) #Fit data to linear modelfit.norm.eb <- eBayes(fit.norm) #Empirical Bayeswrite.csv(fit.norm.eb, file="filename.csv") #write to CSV file
</pre>