Dear colleagues,

I know this package is out-dated. I just want to report this error.

I was using cufflinks 2.2.1. Every thing was fine.

I wanted to used cummeRbund (v 2.24.0) to visualize the results. I had tried cummeRbund on expdata of package and there was no error.

Then I tried it on my data. The error lied in readCufflinks.

Specifically, the error occured at this line: genemelt<-as.data.frame(dcast(genemelt,...~measurement))

The warning and error message were:

Aggregation function missing: defaulting to length
Error in dim(ordered) <- ns : 
 dims [product 23544] do not match the length of object [282517]

I looked into my data, I found this line caused error: XLOC_002304 - - XLOC_002304 ZnT35C TSS2720,TSS2721 2L:15228728-15247832 - - 1.64092 0 3.29494 OK 2.00419 0 4.17461 OK

If I deleted this line, there was no error while calling readCufflinks.

But it was not this line per se that caused the error. If I deleted the line above, the error also disappeared.

Really wierd.