[BioC] how to design comparision using edgeR

[wang peter]

dear all:

my data is composed of 35 samples, have two factor
time and treatment

i want to find DE genes between 6h and 0h due to the treatment
effect,removing the time factor effect.

how can i use glamLRT to do test

raw.data <- read.table("expression-table.txt",row.names=1)
lib_size <- read.table("lib_size.txt");
lib_size <- unlist(lib_size)
d <- DGEList(counts = raw.data, lib.size = lib_size)
dge <- d[rowSums(d$counts) >= length(lib_size)/2,]

#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(~time+treatment)

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

lrt.dge <- glmLRT(dge, glmfit.dge, coef=2)??????????????????????????????



how can i use glamLRT to do test

--
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
Facebook:http://www.facebook.com/profile.php?id=100001986532253


-- 
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
Facebook:http://www.facebook.com/profile.php?id=100001986532253