Hello All,

 I have an RNA-seq experiment with three conditions: A, B, and C. I combined A+B as single condition and did a DE analysis as A+B vs C and I have a set of DE genes (logFC>=1 and padj<=0.05).I want to know which genes are differentially expressed specifically in condition A+B.

I saw a using contrast for this, but i have only two conditions

results(dds, contrast=list("conditionA+B", c("conditionC")), listValues=c(1, -1/2))

I am interested to know whether the above script helps to give the list of DE genes specific for condition A+B. Can this problem be solved in one nice integrated statistical framework that also allows me to nicely rank my resulting DEGs by statistical significance?

hi Alva,

I'd set it up with condition=c("A","B","C") -- with replication obviously -- and use design=~condition.

Then to generate a comparison of (the average of A and B) vs C, you can do:

results(dds, 
        contrast=list(c("conditionA","conditionB"), 
                        "conditionC")), 
        listValues=c(1/2, -1))

Is this what you were looking for?