Different fpkm values for cuffdiff and cuffcompare

[madsaan]

Hi,

I have noticed that some of my FPKM values are 0 in the gene_exp.diff file.I did notice that it was not 0 in the transcripts.tmap file.Does anyone know why does this is happening.

Thanks,
Joji

[IBseq]

hi did find an answer to this?

thanks,
ib

[sqcrft]

I have the same problem, anybody has a clue?

[sdriscoll]

You'd have to ask the authors about this one. I'm not sure why their expression assignment algorithm would make different decisions when cufflinks is run verses when cuffdiff is run.