[BioC] DEXSeq error: Count files do not correspond to the flattened annotation file

[Simon Anders]

Hi Darwin

> FWIW, DEXSeq works on the same data set, but with a slightly
> different flat GFF (the one that gives me trouble have been changed
> the gene names). The GFF is flattened from a Cufflinks GTF.

Wait, what do you mean by "changed the gene names"?

Each count file has two columns, one with the gene IDs, the other with 
the counts. The flattened GFF file also contains the gene ID, and to 
make sure that count files and GFF file fit together, DEXSeq compares 
the gene IDs and complains if they don't match.

   Simon