Question: DESeq2 multiple factor design

I have an experiment where I got 2 factor, the first one is the cell line, and the second one is the treatment.

In this, one cell line is derived from the other, the derived cell line received a inducible gene.

I then treated both cell lines with the inducer or vehicle.

I want to set the factors so DESeq2 compared the mother cell line +/- inducer to obtain the list of genes that are altered by the inducer alone, to the get the list of genes that are altered from the derived cell line +/- inducer and compare to the first result.

as in factors A, B, C and D, I want AxB=AB and CxD=CD, then compare ABxCD.

is that something DESeq2 can do?

I tried setting the factor levels like that:

dds$Cond <- factor(dds$Cond, levels = c("PRH_D","PRH_V","PC3_D","PC3_V"))

and got that:

##[1] "Intercept"           "Cond_PRH_V_vs_PRH_D" "Cond_PC3_D_vs_PRH_D"
##[4] "Cond_PC3_V_vs_PRH_D"

anyone have any tip on how i could set this levels?

keep in mid I am quite new to this.

thanks in advance.

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