Dont use the - b parameter
Sent from my iPhone; please excuse any brevity or typos!
On Nov 15, 2013, at 2:51 PM, clare Hardman chardman@mrc-lmb.cam.ac.uk wrote:
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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