[BioC] find DE by edgeR

wang peter wng.peter at gmail.com
Thu Aug 30 23:29:31 CEST 2012

i try to find DE on each time point
by comparing treated vs control, such is coding
please help me to check if it is right?

thank you very much

group =factor(c('c0h','c0h','c0h','c24h','c24h','c24h','t0h','t0h','t0h','t6h','t6h','t6h','t6h','t12h','t12h','t12h','t12h','t18h','t18h','t18h','t18h',
d <- DGEList(counts = d, lib.size = lib_size, group = group)

d <- calcNormFactors(d)

#To estimate common dispersion:
d <- estimateCommonDisp(d)
#To estimate tagwise dispersions:
d <- estimateTagwiseDisp(d)

#c0h vs t0h
et <- exactTest(d, pair=c("c0h","t0h"), dispersion="tagwise")
result <- topTags(et, n=dim(d)[1], adjust.method="BH", sort.by="p.value")
write.table(result,file = "t0h_c0h",sep = "\t")

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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