CPM function in EDGER
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francesca3 • 0
@francesca3-23121
Last seen 10 months ago
Italy

Hi, I have some doubts on cpm function in edgeR package. Given this initial part of the code:

> library(edgeR)
> data_clean<- read.table("unito.txt", header = TRUE)
> 
> group<-factor(c("A", "A", B","B"))
> 
> y <- DGEList(counts=data_clean,group=group)
> 
> y <- calcNormFactors(y)

I obtain different values if I calculate cpm in this way

> cpm <- cpm(y, log = FALSE, normalized.lib.sizes=TRUE)

Or in this one

> cpm <- cpm(y$counts, log = FALSE, normalized.lib.sizes=TRUE)

Why are them different? What does it change? What is the correct way to calculate them? I noticed that if I calculate them with the standard formula "by hand", I obtain the same values as the second formula (y$counts). In the edge manual it seems just to use the y argument.

Thank you, Francesca

edger cpm rnaseq • 1.1k views
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Cross-posted and answered on biostars: https://www.biostars.org/p/458178/

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Please do not cross-post. This community here is driven by the developers of the tools and therefore intended for specific technical advise towards the packages. The "standard" questions are more suited for Biostars. No need to bother the developers who already invest a lot of time maintaining their tools with non-technical questions. Thank you!

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