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