Hi,

When manually checking p-values from edgeR, I found the p-value of this
gene difficult to understand. The CPM of this gene in our study is like
this:

control replicate1: 0
control replicate2: 0
control replicate3: 0
treat1 replicate1: 0
treat1 replicate2: 0.24
treat1 replicate3: 0
treat2 replicate1: 0
treat2 replicate2: 0.14
treat2 replicate3: 0.19
treat1&treat2 replicate1: 25.14
treat1&treat2 replicate2: 44.36
treat1&treat2 replicate3: 34.62

I fitted GLM with model.matrix(~treat1 + treat2 + treat1:treat2).  To find
out genes under significant interaction effect, lrt <- glmLRT(fit, coef=4)
gives the following results to this gene:

logFC: 5.43
logCPM: 3.19
LR: 0.012
PValue: 0.91

Why do such dramatic change and such large logFC have p-value of 0.91? The
p-values of other manually checked genes make sense to me, but I just
cannot understand the p-value of this one.

I used the latest version of R and edgeR.

Thanks,
Xinwei

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