Thank you both! It helped a lot. I saw that previous response, but I was not sure at all if it would fit for the parameters I was using (in fact, I deduce from @himel.mallick answer that this formula is not proper for linear model, right?). Now I changed the analysis_method to CPLM and transform to NONE, and following the formula I guess I get the log2 fold change correctly.
Thanks again, and keep on doing your excellent job.