I have a simple2x2 design for RNASeq DEG analysis with DESqe2. When I read the manual I got quite confused by the examples provided for the two conditions,two group design.
I. by doing the following, are we trying to find genes expression level differences between conditions A and B or between group Y and X?
" results(dds, contrast=c("condition","B","A")) "
2. By doing the following, are we only trying to find the interactions between two factors"group" and 'condition"?
" results(dds, name="groupY.conditionB") "
3. What is 0, and 1? I might missed something from the manual?
# the condition effect in group B results(dds, contrast=c(0,0,1,1))
4. Are we trying to find gene expression difference between condition A and B or group Y or X, are we considering the interactions between group and conditions?
# or, equivalently using list to add these two effects results(dds, contrast=list(c("condition_B_vs_A","groupY.conditionB")))
5. Wht the resultNames (dds) only show "groupY.conditionB", what if we want to "groupX. conditionB" or more?
Besides, I have a relevel question:
For my 2X2 design, should I relevel both group and condition such as
or just need to relevel one? Because the example only did relevel for one factor, I am afraid if I relevel two, the first relevel (condition) will be replaced by the second level of factor (group)? Or not?
Thank you very much