[BioC] Question if DESeq can still be used after correction for T0?
anders at embl.de
Mon Jun 10 15:05:53 CEST 2013
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
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.
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