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  • Problem with cummeRbund and RSQLite :(

    Hi there, I have a problem in using cummeRbund and the issue is similar with the thread http://seqanswers.com/forums/showthread.php?t=18830 but not the same. Hope anyone can help me to solve this question..

    I use the R(2.15.0) and cummeRbund 1.2.0.
    Code:
    > library(cummeRbund)
    Loading required package: RSQLite
    Loading required package: DBI
    Loading required package: ggplot2
    Loading required package: reshape2
    > cuff<-readCufflinks("cuffdata_120417")
    Creating database cuffdata_120417/cuffData.db
    Reading cuffdata_120417/genes.fpkm_tracking
    Checking samples table...
    Populating samples table...
    Writing genes table
    Reshaping geneData table
    Recasting
    Writing geneData table
    Reading cuffdata_120417/gene_exp.diff
    Error in function (classes, fdef, mtable)  : 
      unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "logical"
    >
    IMO there should be something wrong(format?) in my gene_exp.diff so the RSQLite package aborted. And the cuffData.db do built up but I'm wondering if it is complete..
    Hope for your reply. Thanks ^_^

  • #2
    Please make sure that your sample names are unique and do not have funky characters or begin with numeric values.

    Feel free to contact me directly if you continue to have problems.

    Cheers,
    Loyal

    Comment


    • #3
      Problem solved.

      The reason why cummeRbund stuck is I use the sample name as "T" and R think the T is a logical value "True". When i changed the sample name then the problem solved.

      Thank for Loyal and hope this (stupid unique) question may helpful to others.

      Comment


      • #4
        Hi there ?
        I have the same problem and did the same mistake; trying again with new sample name and will let you know if this sort out the problem.
        Thank you

        Originally posted by lgoff View Post
        Please make sure that your sample names are unique and do not have funky characters or begin with numeric values.

        Feel free to contact me directly if you continue to have problems.

        Cheers,
        Loyal

        Comment

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