Cufflinks, Cuffdiff, without replicates

[brachysclereid]

Hi,

Can anyone help to understand how cufflinks/cuffdiff functions in the absence of replicates in layman's terms? I have read the website a few times and I'm afraid that I am missing something. How is the variance estimated in the absence of replicates for a given gene?

I am trying to figure out the mathematics of why you need a higher log fold change for a gene with low expression to get a significant p-value, whereas for a highly expressed gene a trivial change in fold change results in a significant p-value. It makes a lot of sense intuitively, but I am trying to understand this so that I can actually explain it.

Any help would be appreciated!

[IBseq]

hi did you find any answer?

thanks,ib