Hello,

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")

and

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)
[1] "Intercept"            "stage_20dpd_vs_12dpd"
[3] "stage_4dpd_vs_12dpd"  "stage_D2_vs_12dpd"

My goal is to have the following: 

> resultsNames(dds.t0)
[1] "Intercept"            "stage_D2_vs_4dpd"
[3] "stage_D2_vs_12dpd"  "stage_D2_vs_20dpd"

Can anyone help me figure out where I've gone wrong?

Thanks very much!

I don't know exactly what order you performed these operations, but note that you have to relevel before running DESeq() to impact the resultsNames(dds) output.

relevel() selects the reference level, so the denominator. You will have "stage_...vs_X" for whatever X you you chose as the reference level.

Finally, note that you can extract any comparison you want using the 'contrast' argument. See ?results.