Hi Noa,
Yes I did use Cufflinks so this sounds just like my problem. So how have you
dealt with the problem?
Best wishes,
Clare
On 14 Nov 2013, at 18:17, Noa Sher wrote:
Hi Clare
We just ran into a similar issue about a week ago and were debugging with the
authors of cuffdiff
Apparently there are issues with the -b parameter - were you using this in
cufflinks?
If yes - this may be the cause - we switched the order of the replicates and
the values changed; as did PCA's of the samples, etc
They are working on this issue for an upcoming version of cufflinks.
I am interested in knowing whether this was indeed your problem or were you
using a pipeline that does not include cufflinks?
Good luck,
Noa
On 14/11/2013 13:13, clare Hardman wrote:
Hello,
Could you please advise me on this probably naive question. When I compare
sample A and sample B by Ciffdiff and then separately compare Sample A to
Sample C by Cuffdiff too, should the FMPK value be the same for A in both
tests? At the moment mine does not seem to be!
Best wishes
Clare
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