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  • Palgrave
    Member
    • Aug 2011
    • 73

    #1

    EdgeR compare 3 samples (RNA_Seq)

    I have three subgroup witk 2 or 3 column each. I want to compare the subgroups with each other and print and vizualize differential expressed genes.

    How do I do this using EdgeR?
  • Gordon Smyth
    Member
    • Apr 2011
    • 91

    #2
    The edgeR User's Guide, which comes with the package, gives fully worked start to finish analyses for five case study data sets. There isn't a case study with exactly three groups, but extrapolating from the examples should not be too difficult.

    Best wishes
    Gordon

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