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)
Hi, Gordon Smyth,
Thank you very much for your reply. I re-analyzed my data and now see the identical results. I did something wrong in previous analysis. Thanks!