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  • pca in DESeq2

    Hello,

    I run successfuly using the following code in DESeq2:
    plotPCA(rld, intgroup=c("population", "treatment"))

    However, I would like to use ggplot2 to draw a nice PCA plot as showed in the vignette. I run the following code and encounter a problem:
    data <- plotPCA(rld, intgroup=c("population", "treatment"), returnData=TRUE)

    The error is that the "returnData=TRUE" was not used. Does anybody know how to fix it?

    Thank you in advance.

  • #2
    Check the version of DESeq2 that you're running?

    packageVersion("DESeq2")

    This argument appeared in DESeq2 1.5.27.

    Comment


    • #3
      Thank you for your answer.

      > packageVersion("DESeq2")
      [1] ‘1.4.5’

      It's 1.4.5, although I re-installed DESeq2 from Bioconductor yesterday.

      Comment


      • #4
        You should check your Bioconductor version then.
        You may have to update R first to be able to use the latest Bioconductor version.
        So, I would update R first, then Bioconductor, and finally DESeq2.
        It's a bit of work, but DESeq2 has evolved quite a bit over the different versions.
        It may actually be worth repeating the entire analysis with the latest version of DESeq2.

        I do agree that it is a common source of frustration that you only get the latest version of the package corresponding to your Bioconductor version when you install a package.
        Last edited by blancha; 07-02-2015, 01:00 PM.

        Comment


        • #5
          Originally posted by blancha View Post
          You should check your Bioconductor version then.
          You may have to update R first to be able to use the latest Bioconductor version.
          So, I would update R first, then Bioconductor, and finally DESeq2.
          It's a bit of work, but DESeq2 has evolved quite a bit over the different versions.
          It may actually be worth repeating the entire analysis with the latest version of DESeq2.

          I do agree that it is a common source of frustration that you only get the latest version of the package corresponding to your Bioconductor version when you install a package.
          After installed the latest R, I can install the latest DESeq2. The code works now.
          Thank you very much for your help.

          Comment

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