What will the the classic approach is to make pairwise comparisons between the groups in edgeR?

What will the the classic approach is to make pairwise comparisons between the groups in edgeR?

1

The edge manual I understand

The classic edgeR approach is to make pairwise comparisons between the groups. For example,

et <- exactTest(y, pair=c(“A”,”B”))
will find genes differentially expressed (DE) in B vs A.

Similarly

et <- exactTest(y, pair=c(“A”,”C”))
for C vs A,

or

et <- exactTest(y, pair=c(“C”,”B”))
for B vs C.

I have a query about how to define group and their calculations.

  1. et = exactTest(exp_study, pair=c(“Treatment”, “control”))
    will do calculation
    =Control/Treament

  2. et = exactTest(exp_study, pair=c( “control” ,”Treatment”))
    will do calculation
    =Treament/Control

As I understand from the manual I need to define a group as 2. I am a little unsure about it

Please guide me regarding my confusion about defining group and their calculations.

Thank you!


edgeR

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