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 [[alternative HTML version deleted]]