[BioC] how to make makeContrast in edgeR?

wang peter wng.peter at gmail.com
Sat Aug 25 06:15:38 CEST 2012

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)
dge <- calcNormFactors(dge)
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

shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu

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