Question: edgeR and DESeq2
0
gravatar for yueli7
17 months ago by
yueli70
China
yueli70 wrote:

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!
 

edger deseq2 • 353 views
ADD COMMENTlink modified 17 months ago by Gordon Smyth38k • written 17 months ago by yueli70
Answer: edgeR and DESeq2
0
gravatar for Michael Love
17 months ago by
Michael Love25k
United States
Michael Love25k wrote:

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.

ADD COMMENTlink modified 17 months ago • written 17 months ago by Michael Love25k
Answer: edgeR and DESeq2
0
gravatar for Gordon Smyth
17 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

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.

ADD COMMENTlink written 17 months ago by Gordon Smyth38k

Thanks, Gordon Smyth,

What is the mean of "IMO "?

Thank you!

ADD REPLYlink modified 17 months ago by Gordon Smyth38k • written 17 months ago by yueli70

"In my opinion". Honestly, a Google search would have taken... all of 10 seconds.

ADD REPLYlink written 17 months ago by Aaron Lun25k

yueli7 is based in China, so Google might be blocked ...

ADD REPLYlink modified 17 months ago • written 17 months ago by Gordon Smyth38k
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