What will the the classic approach is to make pairwise comparisons between the groups in edgeR?
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.
-
et = exactTest(exp_study, pair=c(“Treatment”, “control”))
will do calculation
=Control/Treament -
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!
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