Entering edit mode
4.8 years ago
wangdp123
▴
340
Hi there,
It seems that there are two ways of calculating RPKM values based on rpkm function of edgeR from the output of featurecounts. One uses calcuNormFactors and the other doesn't.
I wonder which one is more appropriate for generating RPKM values from RNA-Seq analysis? Why?
1)
x <- DGEList(counts=fc$counts, genes=fc$annotation[,c("GeneID","Length")])
x_rpkm <- rpkm(x,x$genes$Length)
2)
y <- DGEList(counts=fc$counts, genes=fc$annotation[,c("GeneID","Length")])
y <- calcNormFactors(y)
y_rpkm <- rpkm(y,y$genes$Length)
Many thanks,
Tom