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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