Hello. I have a question regarding the results(dds) function for DESEQ2.

I have two conditions I am comparing: Knockout vs Young.

After performing summary of my Deseq analysis,

res <- results(dds)
res
summary(res)

I get young vs Knockout as default. Does this mean the young and KO groups were numerators and denominators in the analysis, respectively?

If I use the code:

resKO_vs_Young <- results(dds, contrast = c("Group", "Knockout", "young"))

Would this allow me to compare the knockout/young expression?

I am trying to interpret the resulting heatmaps and wanted to clarify the results of my code. Thank you so much for this wonderful tool.

Does this mean the young and KO groups were numerators and denominators in the analysis, respectively?

Read over the vignette and workflow first. This is described in those documents.