Hello Irene,

It may be that the reference annotation GTF file was absent or did not have content for the transcript in the Cufflinks run that produced the "0" FPKM results. Then the reference annotation GTF used for Cuffdiff did.

If the Cufflinks documentation about calculations does not align with your expected scientific results, and usage errors are eliminated, then reporting a suspected bug to the tool authors is the next step (only they can make changes to the underlying tool). You can share your history with the tool authors using "Options (gear icon) -> Share or Publish". (The information provided in your original question is not enough to provide a reproducible test case).
contact: tophat.cuffli...@gmail.com
http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results

This reply is to address all of the recent similar questions.

Others are of course welcome to continue to offer advice on any of these threads!

Best,

Jen
Galaxy team

On 8/20/12 3:26 AM, i b wrote:
Dear all,
I have two samples, treated and untreated.
I ran cufflinks and had the following:

treated: 884532
untreat.: 130247

I then ran cuffdiff and look ath transcript diff. expression:

treated: 33
untreat.:2.9
significant:yes

Strangely for another transcripts I have:
Cufflinks: treat_:0
               untreat_: 0

Cuffdiff:  trat_4.4
            untreat_0.2
           significant: yes

How this can be possible?

I had similar results with other transcripts where one one of the two
had 0 cufflinks, and the other one very high but the cuffdiff come out
with NO TEST or OK but not significant

thanks,
ib
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