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  • roll
    Member
    • Aug 2009
    • 38

    what normalization should I do to compare featureCount outcome

    I am using featureCount from Rsubread package. What normalization should I do after running the featureCount? I want to compare reads from 6 different samples.
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478

    #2
    It kind of depends on what you're doing. "Comparing" isn't enough information to give you any good advice. For DE analysis, some sort of library size normalization (TMM or otherwise) would be normal. For visual comparisons, perhaps a variance-stabilization transform would be more useful.

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