No, I did not get reply.
However, I think the variance difference is just caused by numerical reasons. Since I do not have experimental replicate, using cufflinks to estimate the expression only consider the variance from the model, such as the variation resulting from the assignment a read to which isoform or possion distribution. this variance do not have any biological meaning. The true variance should include both the model variance and the biological replicate variance.
In cuffdiff, which compare expression difference from two samples/conditions. I believe it estimate the variance from two different samples/conditions. but in this case, the hypothesis that most genes have similar expression level is not necessarily hold. So I think that is the reason why the variance is larger in cuffdiff result.
What's your opinion?
