Suppose I have gene expression values (not at log2) at pre and post from 3 patients (these are real values):
pre<-c(22.228, 0.002, 0.013) post<-c(0.185, 0.018, 0.009)
I am wondering how to calculate the mean fold change between pre and post:
#mean of fold change mean(post/pre)  3.234 #fold change of mean mean(post)/mean(pre)  0.0095
Seems completely different, which one is the correct or should be calculated other ways?
If I wanted to calculate the log2FC:
#this seems the limma formula mean(log2(post))-mean(log2(pre))  -1.4231 #then back to fold change: 2^-1.4231  0.3729
Why this 0.3729 is so different from either the other two 0.0095 and 3.234? Which way should I use?