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

    Leave a comment:


  • lgoff
    replied
    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

    Leave a comment:


  • christophe
    replied
    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

    Leave a comment:


  • christophe
    replied
    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

    Leave a comment:


  • lgoff
    replied
    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

    Leave a comment:


  • dvanic
    started a topic CummeRbund error without CDS

    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!

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