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
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