y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4)
d <- DGEList(counts=y, group=rep(1:2,each=2), lib.size=colSums(y))
rownames(d$counts) <- paste("gene",1:nrow(d$counts),sep=".")
d <- estimateCommonDisp(d)
plotSmear(d)
# find differential expression
de <- exactTest(d)
# highlighting the top 500 most DE genes
de.genes <- rownames(topTags(de, n=500)$table)
plotSmear(d, de.tags=de.genes)
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