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  • Hi all,
    I am very new to r & DEseq2 but have been following the excellent vignette. I have encountered a problem though. I can create the object rld as per the command in the vignette, but when I try to run PCA as suggested I repeatedly encounter the following error:

    plotPCA(rld, intgroup=c("Fibrosis", "Sample.ID"))

    Error in (function (classes, fdef, mtable) :
    unable to find an inherited method for function ‘plotPCA’ for signature ‘"SummarizedExperiment"’
    I have also tried:
    plotPCA( DESeqTransform(rld ) )
    and get the following:
    Error in plotPCA(DESeqTransform(rld)) :
    error in evaluating the argument 'x' in selecting a method for function 'plotPCA': Error: could not find function "DESeqTransform"
    Can anyone advise?
    Caitriona

    Comment


    • How did you make "rld" and what version of DESeq2 are you using?

      Comment


      • Thanks for replying. I am using DESeq2 1.6.3.
        First I made dds:
        dds <- DESeqDataSetFromMatrix(countData = countData,
        colData = colData,
        design = ~ Organ + Fibrosis)
        then:
        rld = rlog (dds)
        I went on to examine rld using: head(assay(rld)), and it is listed in my environment as a large SummarisedExperiment.
        Caitriona

        Comment


        • hi Caitriona

          It looks like you have a mix of out-of-date and new packages. These often generate conflicts. This can occur if you install Bioconductor packages using install.packages() rather than with biocLite().

          Try this:

          source("http://bioconductor.org/biocLite.R")
          biocValid()

          Comment


          • Hi Michael, Thank you for your reply. I installed packages as suggested, and it's working. Thanks! Caitriona

            Comment

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