Hi,
I would like to use edgeR to estimate the RPKM values. I have (1) read counts files estimated by HTSeq-count, and (2) a transcript length file. I know how to estimate CPM in edgeR, using below command lines. However, I don’t know how to estimate RPKM values based on the files I have. Could you show me how to run the command lines in edgeR? Many thanks.
Best,
Gary
Transcript count files
http://68.181.92.180/~Gary/temporal/T8_Early_R_T.txt
http://68.181.92.180/~Gary/temporal/T8_Late_R_T.txt
http://68.181.92.180/~Gary/temporal/T9_Early_R_T.txt
http://68.181.92.180/~Gary/temporal/T9_Late_R_T.txt
Transcript length file
http://68.181.92.180/~Gary/temporal/hg19refGene20160206_TranscriptLength.txt
> targets=readTargets()
> targets
files group description
1 T8_Early_R_T.txt Early T8_Early_R_T
2 T8_Late_R_T.txt Late T8_Late_R_T
3 T9_Early_R_T.txt Early T9_Early_R_T
4 T9_Late_R_T.txt Late T9_Late_R_T
> d=readDGE(targets,skip=0,comment.char="!")
> keep=rowSums(cpm(d)>1)>=2
> d=d[keep,,keep.lib.sizes=FALSE]
> d=calcNormFactors(d,method="TMM")
> dim(d)
[1] 8202 4
> detags=rownames(d)
> detagsfile=cpm(d)[detags,]
> write.table(detagsfile,file="CPM_MSC_8202ene.txt")
> rpkm<-rpkm(d)
Error in rpkm.DGEList(d) : Gene lengths not found
> rpkm<-rpkm(d,gene.lengths)
Error in rpkm.DGEList(d, gene.lengths) : object 'gene.lengths' not found
Hi Aaron,
Thank you so much.