Dear all,

I am new using edgeR to compare two samples, each of which has three replicates.  My code is as follows.  However, I found that if ommiting coef=2 in the code qlf <- glmQLFTest(fit, coef=2) produces much different result.  Why it is so different with and without coef=2?

I really appreciate your help.

d <- read.delim("input", sep = ' ', header=F, row.names=1) 
colnames(d) <- c("w1", "w2", "w3", "m1", "m2", "m3") 
g <- factor(c(1,1,1,2,2,2)) 
dge <- DGEList(counts=d,group=g) 
dge <- calcNormFactors(dge) 
design <- model.matrix(~g) 
dge <- estimateDisp(dge, design) 
fit <- glmQLFit(dge, design) 
qlf <- glmQLFTest(fit, coef=2) 
topTags(qlf, n=100000)

Actually, the results from glmQLFTest() will be identical whether or not you omit coef=2. The default value for coef is the number of columns of the design matrix, which in this case is 2. So I suggest that you recheck your results because it would seem that you have collated your results incorrectly.