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  • 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.

  • #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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