Hello,

I used the edgeR and DESeq2 to calculate the differentially expressed genes.

Of course, the results are not identical. I read many papers, and both of the packages are evaluated quite good.

My question is, what I can do?

Is that possible I can get the intersection or the union of the data?  Or any other way?

Thanks in advance!
 

This question has been asked here before on the support site. In my opinion, there’s not much point asking the package authors which package they prefer. So I don’t comment substantively on these posts.

Why did you do two independent analyses of your data? What did you hope to achieve by doing that?

I always advise users to choose a good DE method and use that. Doing your own ad hoc combination of different methods, in a way not intended by the package authors, is IMO not a good idea.