I want to use the rpkm normalization function to 11 datasets that contain three columns each (gene ID, gene counts and gene lengths). The samples are in 4 groups and I use the following lines:
> y <- dir(pattern="*\.csvReadCount,lib.size=TRUE)
I am getting the following error
> dim(y) NULL > RG<-DGEList(counts=yReadCount : $ operator is invalid for atomic vectors
When I use readDGE, but also I get the error below:
G<-readDGE(y, group=group, labels=NULL) Error in `[.data.frame`(d[[i]], , columns) : undefined columns selected
Thanks in advance for any help you can provide me.