Question: How to set group in EdgeR and DEseq2?
gravatar for deb0612
10 weeks ago by
deb061210 wrote:

I got a sample sheet like this:

 name condition  
 sampe1    T  
 sampe2    T  
 sampe3    N  
 sampe4    T  
 sampe5    N 
 sampe6    N 
 sampe7   N

(T:tumor, N:normal)

When I use this condition in DEseq2, it will use N vs T as default.

If I set group <- factor(c(1,1,2,1,2,2,2)) in EdgeR. It will get opposite result to DEseq2.

I would like to know. If I want to get the up-down regulated gene in Tumor sample.

Should I set tumor as "1" or "2" in EdgeR ?

edger rna-seq deseq2 R • 115 views
ADD COMMENTlink modified 9 weeks ago by nilislam30 • written 10 weeks ago by deb061210

And beware of the using of "T" and "F" as they can be considered as TRUE and FALSE into R

ADD REPLYlink written 9 weeks ago by Antonio R. Franco4.5k
gravatar for Antonio R. Franco
9 weeks ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

It it not important the way you name your factors as long as you can separate and group your samples. You can name factor as letters or as numbers

But at the time of doing the DE analysis, it matters the ORDER you define that factor when the DE analysis is requested. By default, DESEq2 order that factors alphabetically, being used as "control" the first one. You need to use the relevel() function to change your factors if they are not in the order you desire.

In other words. Try to control the way your factors are defined and used in the analysis

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Antonio R. Franco4.5k
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