Hi all, I am using edgeR to find DEG. I have paired samples for cancerous tissue and adjacent non-cancerous tissue.
> type <- factor(c("benign", "tumour", "benign", "tumour", "benign", "tumour") > subject <- factor(c(1, 1, 2, 2, 3, 3)) > design <- model.matrix(~subject+type) > keep <- filterByExpr(y) > y <- y[keep, , keep.lib.sizes=FALSE] > y <- calcNormFactors(y) > fit <- glmQLFit(y,design) > qlf <- glmQLFTest(fit)
Then I used
glmQLFTest and got the below result for one gene for example
> Gene logFC logCPM F PValue FDR > ENSG00000165186.12|PTCHD1 -4.570433395 5.571673968 88.74868282 2.53E-09 6.31E-06
What I'm trying to understand for the
logFC in which condition is it down-regulated? Looking at the cpm table output, I can't see in which condition it is down-regulated (or up-regulate).