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  • CummeRbund error

    Hi,

    I'm running cummeRbund and can't get around this error:

    library(cummeRbund)
    setwd ("<path>")
    cuff_data <- readCufflinks('diff_out')
    csDensity(genes(cuff_data))
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (error in statement: database is locked)

    Does anyone know a solution to this problem?

    R v. 2.15.0
    Cufflinks v. 1.3.0
    CummeRbund v. 2.15.0

    Thanks,

    Nick

  • #2
    Originally posted by NRiddiford View Post
    Hi,

    I'm running cummeRbund and can't get around this error:

    library(cummeRbund)
    setwd ("<path>")
    cuff_data <- readCufflinks('diff_out')
    csDensity(genes(cuff_data))
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (error in statement: database is locked)

    Does anyone know a solution to this problem?

    R v. 2.15.0
    Cufflinks v. 1.3.0
    CummeRbund v. 2.15.0

    Thanks,

    Nick
    Hi Nick,
    I have seen this error only once before and the issue in this case was that the database was on an NFS mount that was interfering with the normal operation of the SQLite database. Is your working directory also on an NFS mount? If so, is it possible to try and move the directory to a different mount and see if this resolves the error?

    -Loyal

    Comment


    • #3
      Thanks lgoff,

      I've been away from the computer for the past few weeks, but will give this a go and let you know.

      Best,

      Nick

      Comment


      • #4
        HI, anyone has ever had this error?No idea what to do...any suggestion??All my samples have worked except this one...

        > library(cummeRbund)
        Loading required package: RSQLite
        Loading required package: DBI
        Loading required package: ggplot2
        Loading required package: reshape2
        > cuff<-readCufflinks("~/Cuffdiff/hpv18")
        Creating database ~/Cuffdiff/hpv18/cuffData.db
        Reading ~/Cuffdiff/hpv18/genes.fpkm_tracking
        Checking samples table...
        Populating samples table...
        Writing genes table
        Reshaping geneData table
        Recasting
        Writing geneData table
        Reading ~/Cuffdiff/hpv18/gene_exp.diff
        Error in function (classes, fdef, mtable) :
        unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "integer"

        thanks,
        ib

        Comment


        • #5
          CummeRbund error

          Hi
          I have recently installed R and cummeRbund but I dont know how to use it.

          I have completed my tophat followed by cufflinks run on server. and I am using desktop for R within :
          > getwd()
          "C:/Documents and Settings/Charitra/My Documents"

          > cuff_data <- readCufflinks('diff_out')
          > csDensity(genes(cuff_data))
          Error in sqliteExecStatement(con, statement, bind.data) :
          RS-DBI driver: (error in statement: near ")": syntax error)

          can someone tell me which files are to be kept in my working directory from Cufflinks results....??? to produce followings:

          1. Plot the distribution of expression levels:
          > csDensity(genes(cuff_data))
          2. Compare the expression of each gene in two conditions with a scatter plot
          > csScatter(genes(cuff_data), 'C1', 'C2')
          3. Create a volcano plot to inspect differentially expressed genes:
          > csVolcano(genes(cuff_data), 'C1', 'C2')
          4. Plot expression levels for genes of interest with bar plots (Fig. 9a):
          > mygene < - getGene(cuff_data,'regucalcin')
          > expressionBarplot(mygene)
          5. Plot individual isoform expression levels of selected genes of interest with bar plots
          > expressionBarplot(isoforms(mygene))

          I followed Coe Trapnell, Nature Protocol for Vol.7 No.3 | 2012
          Please help me oout if you can ?

          Comment


          • #6
            did you solve it?

            Hi Charitra,

            Did you mennage to solve the problem; I am having the same.

            Thanks a lot,
            Guy

            Comment

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