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  • sdriscoll
    replied
    indeed. i tried this today and the difference in FPKM values between the two normalizations was constant out to 4 decimal places.

    Leave a comment:


  • deepsea
    replied
    Oh I am very sorry! It is my problem: one set was processed slightly differently. :-(

    Thanks, sdriscoll!

    Leave a comment:


  • sdriscoll
    replied
    sounds fishy. i wanna try this out and see what results i get. I'll report back unless of course someone comes in an explains it.

    Leave a comment:


  • deepsea
    started a topic cufflinks --compatible-hits-norm

    cufflinks --compatible-hits-norm

    Hi,

    I am testing cufflinks with two different normalization methods: total-hits-norm and compatible-hits-norm. My understanding is that the only difference between these two methods is the FPKM denominator: one is the number of all hits, the other is the number of hits within the reference GTF. So the ratios of FPKM values calculated by two methods should be a single fixed number, which is the ratio of hits. But, the ratios I got is a distribution. Anybody have an idea of the exact meaning of compatible-hits-norm? Thanks!

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