I got a differentially expressed gene, with log(mean CPM) = 2.2447; logFC = 11.2344; p-adjusted = 0.0016;

This looks neat. But the problem araises when I take the tpm (transcript per million) values of these samples in 2 groups and draw boxplots.

Attached is a boxplot.

It turns out that the medians of both groups are ZERO, and visually, these two groups should not be called different at all!

Here are the two arrays that I used for boxplot: 

[0,0,0.0363,0,0,0,0,15.1621,0,0,0,0.091,13.1992,0,0.064,0,0,27.9052,15.4516,0,0,0,22.6814,0,0.0124,5.3274]

 [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]

Here is the boxplot picture https://drive.google.com/open?id=0B0AM3r3EIYRUVl8zNFphWWJCbEk (somehow can't attached to this form)

Has anyone already encountered this problem? And I would like to know how to justify this case (statistical package edgeR calls it differential expressed, but it's clearly not -- visually). 

Thanks. 

SnowRu

The statistical tests in edgeR don't care about the median. If you have two groups, then edgeR will test the null hypothesis that the mean count (normalized by effective library size) is equal between groups. In your case, the means are clearly different as one of the groups has all-zero expression and the other group has many samples with non-zero expression. The data provides evidence against the null hypothesis; ergo, you get a low p-value.

agree, but if you present this boxplot to your audience, you will have very hard time persuading them that this gene is differentially expresses.