[BioC] Question if DESeq can still be used after correction for T0?

[Simon Anders]

Cor,

Sorry, this may not have been the answer to your question; let me try again.

If I understand you right, your set-up is this: You have two cell lines 
(A and B), and for each of which you have three types of samples, namely
- base line, i.e. before any treatment or incubation (B0)
- incubated for 7 days without drug (U7)
- incubated for 7 days with drug (T7)

Now, the effect of the drug on cell line A (after 7 days) is

    effect_on_A = (T7_A / B0_A) / (U7_A / B0_A) = T7_A / U7_A

as your wrote in your mail.

Similarily, the effect on B is

effect_on_B = (T7_B / B0_B) / (U7_B / B0_B) = T7_B / U7_B


What would be now the difference (or: ratio) between the effect on An 
and on B?

    effect_on_B / effect_on_A = (T7_B / U7_B) / (T7_A / U7_A)

So, for this question, you still don't need the base-line samples.

To find genes whose reaction to the drug is different between the two 
cell lines, you hence compare the models

    count ~ cellLine + treatment

and

    count ~ cellLine * treatment

where the factor "cellLine" has the two levels "A" and "B" and 
"treatment" has the two levels "T7" and "U7".


So, maybe I am confused but I am now unsure whether one needs the 
base-line samples at all.

   Simon