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:
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).