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  • Can edgeR do trend anaysis?

    In edgeR we have found DE genes beween two categorical groups .
    Now the group has 3 levels, we want to see if there is a trend for these DE analysis. How to do it?

  • #2
    Just put the numerical levels into a column of the design matrix:

    x <- numerical values
    design <- model.matrix(~x)

    Then do DE analysis for this coefficient.

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