find the genes differentially expressed in 3 categories of samples

Question

[biostarsb]

Hello; I have a set of data composed of a heterogeneous population of patients

I would like to know if there is a way to find the genes differentially expressed in 3 categories of samples

Sample1 sampe2 ............................... sample20 .. ................... sample26 ............ sample60 G1 G2 . . . . G30000

Knowing that:

~ from sample1 to sample20 it is a class 1 
 ~  from sample20 to sample26 it is a class 2 
 ~   from sample26 to sample60 it is a class 3

with DESeq2 we can compare only 2 classes so we can find only DEG between classe1 and classe2, classe2 and classe3 or classe3 and classe1

is there anther tools that help me to find genes expressed only in classe1 and not in 2 and 3

genes expressed only in classe2 and not in 1 and 3

genes expressed only in classe3 and not in 1 and 3

Thank you!

[theobroma22]

In limma you can make a contrasts matrix to do what you want.

Answer 1

[EVR]

HI,

You can find the Diff expressed genes as you said using DESeq2 and later you compare the results between CLass1, CLass2 and Class 3 using VennDiagrams(http://bioinfogp.cnb.csic.es/tools/venny/)

Answer 2

[guillaume.rbt]

Hi,

I add the same analysis to do between 3 samples.

I used Trinity Differential expression and it worked well.