I'm using interaction terms for DGE analysis I'm doing using DESeq2. I have a case and control group (SA and CTRL, respectively) and males and females per group (Male, Female). I would like investigate sex differences between cases and controls. Here is the design formula:
dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ Age_scale + pH_scale + Sex + Group + Sex:Group
However, I'm having trouble truly understanding what goes on when obtaining results in the presence/absence of using
To explain myself more clearly, what is the difference between:
1) Using no specified contrast when obtaining results. I understand that DESeq2 takes by default the last term, so, you have the results of the interaction effect alone. It is my understanding that what is happening here is: group effect in the female group - the group effect in the male group (group effect is SA vs CTRL). (Male and CTRL as references).
2) Using for example
contrast=list( c("Group_SA_vs_CTRL", "SexFemale.GroupSA"))) when obtaining results.
In my mind, 2 is identical to 1. But is that actually true? Can someone explain to me the precise steps/differences in how results are determined, if there are any?