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nadschro / synergy-analysis

Step by step analysis framework and experimental design for evaluating synergy driving gene expression
MIT License
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Contrast matrix doubt #2

Open GuiSeSanz opened 8 months ago

GuiSeSanz commented 8 months ago

Dear authors,

First of all, thank you very much for this great work and methodology!

I have some questions to create the contrast matrix... as I understand in your example, you have two different methods to perturb the gene expression, the CRISPR and the shRNA. You have two different controls, one for the shRNA perturbation (ctrl), and the other for the viral protein from CRISPR and the shRNA (all.ctrl). Shouldn't you aso have a control for only the VPR?

Also in our experimental design, we are working with SKO and DKO generated by CRISPR. We only need one type of control (WT), or do we need SKO.ctrl and DKO.ctrl?

In the case where we only need one WT, to model the synergy, it should be something like that? Synergy = (DKO_1_2 - ctrl) - ((SKO1 - ctrl) + (SKO2 -ctrl))

Thanks in advance!

doliv071 commented 6 months ago

Your contrast is equivalent to the following since your ctrl cancels out in the second part Synergy = (DKO_1_2 - ctrl) - (SKO1 + SKO2)