[BioC] about edgeR

[wang peter]

hello all
i have such coding

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*time) #


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)

my question is how can estimateGLMCommonDisp be used to get the common
dispersion,
        the glm is only used to get the regression coefficients.
-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
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