I used limma to conduct a differential analysis. Everything worked fine but I can't seem to find something that explains what is going on behind the scenes. How does limma calculate the logFC? I have three replicates in my data and I applied limma (contrast) to the full dataset as well as per replicate. For the most part I get the same logFC but some of them are different. Can someone explain how limma calculates the logFC? Is there a formula I can refer to?
Thanks in advance!