Question: Why all of the logFC are NA in my edgeDF2
gravatar for xuertowong
2.5 years ago by
xuertowong0 wrote:
> countDF2 <- read.delim("countDFeByg2.xls", row.names=1, check.names=FALSE)
> targets2 <- read.delim("mvmtarget1.txt", comment="#")
> cmp2 <- readComp(file="mvmtarget1.txt", format="matrix", delim="-")
> edgeDF2 <- run_edgeR(countDF=countDF2, targets=targets2, cmp=cmp2[[1]], independent=FALSE, mdsplot="")


After i ran this code, all of the logFC in edgeDF2 are NA. But other countDFeByg file are not like the countDFeByg2.xls. Why?

edger R systempiper • 445 views
ADD COMMENTlink written 2.5 years ago by xuertowong0

If i delete many samples, the logFC can be a number. I really dont konw why? Someone help me


ADD REPLYlink written 2.5 years ago by xuertowong0

I'm an edgeR author, but you're using edgeR by way of systemPiper and it's hard to know what systemPiper is doing internally. So the systemPiper author will need to help you.

edgeR does not normally give NA logFCs when used directly.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Gordon Smyth38k
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