Hi,

I have the output files from cufflinks which I am now trying to analyze using cummeRbund for differential splicing, but I have trouble importing my data. 

I used the following code:

> cuff <- readcufflinks()

> cuff

CuffSet instance with:

0 samples

0 genes

0 isoforms

0 TSS

0 CDS

0 promoters

0 splicing

0 relCDS

Could you please tell me what the problem is.

PS The output files are not empty