I have a doubt regarding the logFC calculation in limma. I searched for the answer in Biostars but I have not found anything that help me to understand my doubt. Supposedly logFC is: LOG2(mean (Group A) / mean (GroupB)) Meaning that if a gene logFC has an expression of 50 in Group A and 100 in Group B, the log2 FoldChange would be -1. Thus, the gene would be two times more expressed in Group B. However, I have checked the logFC that appears in the topTable obtained with the functions in limma and the logFC seems to be something else. Here, the logFC represents the difference between the mean of the groups. The value is then elevated to 2 and log transform, to address correctly the difference between the groups. Thus, the value indicates directly the difference between the two groups, it is not the ratio between the groups. So, it is the value of the topTable a proper logFC? Or should I calculate the logFC manually? Maybe I am confused with the terminology and the value of limma is called something else or the "supposedly logFC" that I addressed is named differently.
Thank you for your precious time.