I've recently started using DESeq2 version 1.20. Since there were several changes, I decided to start my pipeline from scratch.
In my design, I have two variables (treatment + infection). To make it easier, I created a variable of the grouping of two variables:
levels(dds$group)  "treated_Inf" "treated_NonInf" "untreated_Inf" "untreated_NonInf"
What I understand from the pipeline, you can either:
- relevel the variable before using DESeq, to get the right variables to compare
dds$group<-relevel(dds$group,ref="untreated_NonInf") levels(dds$group)  "untreated_NonInf" "treated_Inf" "treated_NonInf" "untreated_Inf"
- use the argument contrast in results, to compare levels that are not reference.
res<-results(dm,contrast = c("group","untreated_Inf","untreated_NonInf"))
As far as I get it, these two comparisons should produce the same results or (at least) similar results. This happens in most cases; however, there are some specific DE genes that become non-DE. For what I understand, this shouldn't happen.
Shouldn't I get the same results? Or am I doing something wrong?