I'm doing expression profiling analysis and I know that the log2fc indicates how much changes the expression of a condition compared to another.
If I have two condition where one is treated and one is untreated, and I set as reference level the treated contitions, the output of DESeq2 refers how many folds the treated contition changes over the untreated, is it correct?
I have this doubt ..
If you set treated as the reference level, as you have done, then a positive log (base 2) fold change means higher expression in untreated. That is, the reference level becomes the denominator in the fold change calculation - everything else is the numerator.
You can easily verify this via a box and whisker plot where you stratify expression of a gene across your 2 conditions, e.g.:
Thank you for the clarifying Kevin