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)