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  • IBseq
    replied
    hi did you find any answer?

    thanks,ib

    Leave a comment:


  • brachysclereid
    started a topic Cufflinks, Cuffdiff, without replicates

    Cufflinks, Cuffdiff, without replicates

    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!

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