Hello,

Would you be able to share a history containing these data? Use "Options (gear icon) -> Share or Publish", generate the share link, then copy and paste that into a reply email sent to me directly. Please note the dataset #'s for the Cuffdiff runs that you are comparing and make sure that all inputs are undeleted.


Best,

Jen
Galaxy team

On 10/12/12 9:43 AM, i b wrote:
Hello forum,
I have ran cuffdiff with two samples, treated vs untreated, and had
certain values as expressed in the output (isoform differential
expression).

When I ran it again, using a different treated sample, but SAME
UNTREATED SAMPLE, the values assigned to the untreated are different.

Why is this if values are calculated from a unique FPKM? This happend
for other jobs where I have ran the same untreated vs other treated
samples...

Thanks a lot,
ib
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