I am so new in using R and edgeR. I calculated the logFC in edgeR using the following code:
targets <- read.delim("cell_line_M.txt", stringsAsFactors = FALSE)
d <- readDGE(targets)
colnames(d) <- c("MG1","MG2", "MN1","MN2")
d <- estimateCommonDisp(d, verbose=TRUE)
d <- estimateTagwiseDisp(d, trend="none")
et <- exactTest(d,pair=c("MN","MG"))
print(et)
this is what I obtained :
logFC logCPM PValue
A1CF 0.20103589 4.718215 0.8603790511
my problem is how the logFC is calculated. the main file is
gene MG1 MG2 MN1 MN2
A1CF 8 7 7 4
I expect that the logFc should be calculated from the strategy suggested in here like:
FC=sqrt(87)/ sqrt(74) --> logFC=log2(FC) = 0.49
but edgeR suggest logFC=0.2
Can anyone guide me if in a wrong way I am or i missed anythong?
Linking to duplicate post: Calculation of logCPM in edgeR