Hi cristophe,
This was a bug inadvertently created when I switched to reshape2. I have fixed it for future releases, but for now, the workaround is to import the original 'reshape' library before calling 'readCufflinks':
Code:
>library(cummeRbund)
>library(reshape)
>cuff<-readCufflinks()
Let me know if this doesn't work.
Cheers,
Loyal