Thanks very much Mike. This has been very very helpful. Let me strike the iron while it's hot once for all, please bear with me one more time.

> As you have a clear base level of treatment (vehicle), I'd recommend
> using a standard model matrix with base levels of C1 and TVeh. I will
> make a note to include more documentation on this option.
> 
> dds$celltype <- relevel(dds$celltype, "C1")
> dds$treatment <- relevel(dds$treatment, "TVeh")
> dds <- DESeq(dds, modelMatrixType="standard")

This was very clear in the current documentation (v1.4.5). This was indeed what I did, but didn't include in the original post to cut down the length. 

>
> After this, you can test if the T1 effect is different in celltype 2
> with the interaction:
> 
> results(dds, name="celltypeC2.treatmentT1")
Got it. My mistake was to ignore the implicitly defined base levels, and was doing:
results(dds,contrast=list("celltypeC2.treatmentT1","celltypeC1.treatmentT1"))
Out of curiosity, what does my contrast statement above do, if sensible at all?

> 
> The T1 effect in celltype 1 (the main effect, as celltype 1 is the
> base level) is:
> 
> results(dds, contrast=c("treatment","T1","TVeh"))
Clear.

> 
> The T1 effect in celltype 2 is the main effect above plus the interaction:
> 
> results(dds, contrast=list(c("treatment_T1_vs_TVeh","celltypeC2.treatmentT1"),character()))
syntax-wise, will this be?
results(dds,contrast=list(c("treatmentT1","celltypeC2.treatmentT1"),character()))

additional questions:
1) to compare baseline (Veh) DEs b/w two cell lines:
results(dds,name="celltypeC2") or 
results(dds,contrast=list(c("celltypeC2","celltypeC2.treatmentVeh"),
                                   c("celltypeC1","celltypeC1.treatmentVeh"))

2) if I have 3 treatments in total, T1, T2, T3, plus TVeh, and I want to compare T1 vs. T2 in C2, would i do:
results(dds,contrast=list("celltypeC2.treatmentT1","celltypeC.treatmentT2"))

-Rob


 		 	   		  
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