Why all of the logFC are NA in my edgeDF2

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xuertowong • 0

@xuertowong-12545

Last seen 7.7 years ago

> 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?

R edger systemPipeR • 1.4k views

ADD COMMENT • link 7.7 years ago xuertowong • 0

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

ADD REPLY • link 7.7 years ago xuertowong • 0

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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 REPLY • link 7.7 years ago Gordon Smyth 51k

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