edgeR comparison of 2 samples

Question

[biology_inform]

Hi

data <- readDGE(files) 
data <- head(data, -5) group <- c(rep("wt", 3),rep("res", 3)) 
dge = DGEList(counts=data, group=group) 
dge <-calcNormFactors(dge) 
dge <- estimateDisp(dge)
et <- exactTest(dge, pair=c("wt", "res")) 
write.csv(et$table,"dacomitinib-edgeR.csv")

I am analyisng my sample rnaseq data with EdgeR and with this code above; I wonder that am I comparing wt vs res or res vs wt? Where can I understand this thanks:)

Answer 1

[Carlo Yague]

A stated in the manual,

exactTest(dge, pair=c("wt", "res")) 

will find genes differentially expressed (DE) in "res" vs "wt".