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