[BioC] how to make makeContrast in edgeR?

[wang peter]

I meet such problem, this is the coding

raw.data <- read.table("expression-table.txt",row.names=1)
lib_size <- read.table("lib_size.txt");
lib_size <- unlist(lib_size)
d <- raw.data[, 2:dim(raw.data)[2]]
length<-raw.data[, 1]

d <- DGEList(counts = d, lib.size = lib_size)
#normalization
dge <- calcNormFactors(dge)
treatment=factor(c(rep('control',6),rep('treated',24),rep('control',5)))
time=factor(c('0h','0h','0h','24h','24h','24h','0h','0h','0h','6h','6h','6h','6h','12h','12h','12h','12h','18h','18h','18h','18h',
             '24h','24h','24h','36h','36h','36h','48h','48h','48h','6h','12h','18h','36h','48h'))
design <- model.matrix(~treatment*time)

dge <- estimateGLMCommonDisp(dge, design)
dge <- estimateGLMTagwiseDisp(dge, design)
glmfit.dge <- glmFit(dge, design, dispersion=dge$tagwise.dispersion)

i want to make contrast between 6h_treated vs 6h_contol, 12h_treated
vs 12h_contol,
and so on....

how to use makeContrast or any other function to compare them

thank you very much

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shan gao
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Boyce Thompson Institute
Cornell University
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