I am trying to find differentially expressed genes using DESeq2 on some RNA-seq data. In the pheno data, there is a column named 'condition' with factored values of 'Treated' and 'Untreated'. I want to use just this column for my experiment.

However, when I use the results() function in DESeq2 with my data, I get the first line as: 'log2 fold change (MLE): condition Untreated vs Treated'

Now, I am new to this, so I am not sure if this is the same as 'Treated vs Untreated' or not. And I don't know why it decided to show 'Untreated vs Treated'.

I would love some clarification. Are the 2 things (A vs B and B vs A) the same? If not, what does each one mean? and how to control what is compared?

exp_1 = DESeqDataSetFromMatrix(
  countData = Counts,
  colData = Phenotypic[match,],
  design = ~ condition
  )

my_deg = DESeq(exp_1)

fin_results = results(my_deg, alpha=0.05)

This is covered in the vignette (note on factor levels).