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  • rondon
    Junior Member
    • Aug 2014
    • 5

    #1

    FPKM in DESeq2

    Hi guys, I'm using DESeq2. I'd like to see the FPKM, and It should be easy as
    > my_fpkm <- fpkm(dds)
    But I need do merge the genes sizes data to dds, and I don't know how to do it. Can anyone help me?
    I have a table with genes IDs and genes lengths.

    my best regards.
    Last edited by rondon; 07-09-2015, 09:13 AM.
  • fanli
    Senior Member
    • Jul 2014
    • 197

    #2
    Something like this:
    Code:
    mcols(dds)$basepairs <- gene_sizes[, "length"]
    assuming gene_sizes is your table.

    Comment

    • rondon
      Junior Member
      • Aug 2014
      • 5

      #3
      That's it! Thank you very much!

      Comment

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