I have some questions about releveling to reset the factor level.
I am running an experiment in DESeq2 with 4 stages that I want to compare to each other under one treatment. My goal is to change which factor is the reference for generating result outputs. I understand that the default is the 1st factor, by alphabetical order. I have tried releveling with both of the following ways:
dds.t0$stage <- relevel(dds.t0$stage, "D2")
dds.t0$stage <- factor(dds.t0$stage, levels=c("D2", "4dpd", "12dpd", "20dpd"))
However, both of these still return the same default resultsNames list:
> resultsNames(dds.t0)  "Intercept" "stage_20dpd_vs_12dpd"  "stage_4dpd_vs_12dpd" "stage_D2_vs_12dpd"
My goal is to have the following:
> resultsNames(dds.t0)  "Intercept" "stage_D2_vs_4dpd"  "stage_D2_vs_12dpd" "stage_D2_vs_20dpd"
Can anyone help me figure out where I've gone wrong?
Thanks very much!