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  • CummeRbund error without CDS

    Hi! I'm trying to run cummeRbund on a cufflinks dataset without a reference annotation of any sort (i.e. just the transcripts assembled from bowtie/tophat results), which leads to my cds.diff being empty.
    Hence, I get the following error when trying to create a cummeRbund database:

    Writing CDS table
    Error in sqliteExecStatement(con, statement, bind.data) :
    bind.data must have non-zero dimensions
    How do I get around this (other than by using a reference annotation)? I'd still like to be able to explore the gene/tss/isoform information?

    Thanks in advance!

  • #2
    Hi dvanic,
    This has been addressed in the development version of cummeRbund. (now v1.1.3). Please try updating to the new version and see if this resolves this issue.

    compbio.mit.edu/cummeRbund

    Cheers,
    Loyal

    Comment


    • #3
      Hi loyal Goff,
      I have been trying running CummeRbund. As suggested I installed the latest version of cummeRbund (v1.1.3) within R 2.15.0 . The Error << Error in data.frame(index = c(1:length(samples)), sample_name = samples) arguments imply differing number of rows: 2, 0
      Calls: readCufflinks -> loadGenes -> populateSampleTable -> data.frame
      >>
      disappeared , but a new one showed up as copied below:
      NOTE: my working directory is the ouput directory of cuffdiff. I have to mention that CDS, promoter and TSS files are empty in my case. Only Isoforms and Genes files contain results.



      Loading required package: RSQLite
      Loading required package: methods
      Loading required package: DBI
      Loading required package: ggplot2
      Loading required package: reshape2
      Creating database /cuffdiff_outputs/cuffData.db
      Reading /cuffdiff_outputs/genes.fpkm_tracking
      Checking samples table...
      Populating samples table...
      Writing genes table
      Reshaping geneData table
      Recasting
      Error in as.data.frame(cast(genemelt, ... ~ measurement)) :
      could not find function "cast"
      Calls: readCufflinks -> loadGenes -> as.data.frame



      Thanks for your help.
      Best,
      Christophe

      Comment


      • #4
        Addendum to my previous post:
        I have tried to run cummeRbund both on linux and Windows and got the same error:

        Error in as.data.frame(cast(genemelt, ... ~ measurement)) :
        could not find function "cast"
        Calls: readCufflinks -> loadGenes -> as.data.frame
        Execution halted

        Comment


        • #5
          Temp fix

          Hi cristophe,
          This was a bug inadvertently created when I switched to reshape2. I have fixed it for future releases, but for now, the workaround is to import the original 'reshape' library before calling 'readCufflinks':

          Code:
          >library(cummeRbund)
          >library(reshape)
          >cuff<-readCufflinks()
          Let me know if this doesn't work.

          Cheers,
          Loyal

          Comment


          • #6
            Hi Loyal,
            That works.
            Only reshape2 was loading automatically and not reshape.
            Thanks
            Christophe

            Comment

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