Hi Gondon,Bioconductor experts,

I have RNA-seq data for 3 genotypes(each genotype having 3 biological
replicates) and 30,000 genes.
I was trying to find out differentially expressed genes across all
genotypes. Here is the code I am using.

 library(edgeR)
y<-read.table('test_12339.txt'
)
 d <- DGEList(y, group = rep(1:3, each = 3), lib.size = lib.sizes)
 d <- calcNormFactors(d)
 times <- rep(c("p1","p2","f1"),c(3,3,3))
 times <- factor(times,levels=c("p1","p2","f1"))
 design <- model.matrix(~factor(times))
disp <- d2$tagwise.dispersion
 fit <- glmFit(d,design,dispersion=disp)
 lrt <- glmLRT(d,fit)
topTags(lrt)

Does this code provide me with tags differentially expressed across all
conditions? (I am not looking for pairwise differential expression
but across all conditions)

Thanks,
Shreyartha

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