Hello,
Thank you for sharing your history. The difference in FPKM values can be
explained by the use of the -N option (Perform quartile normalization:
Yes). Set this to No to avoid the variable per-run normalization.
This has also been discussed at seqanswers.com:
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
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
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