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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