Dear all, I have two samples, treated and untreated. I ran cufflinks and had the following FPKM:

treated: 884532 untreat.: 130247

I then ran cuffdiff and look at the transcript diff. expression values:

treated: 33 untreat.:2.9 significant:yes

Strangely for another transcripts I have the following FPKM: Cufflinks: treat_:0 untreat_: 0

Cuffdiff values: 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