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  • [solved]cummeRbund error message

    Running cummeRbund gives me the following error:

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


    Anyone know why? It workes with a different sample.
    Last edited by Palgrave; 10-17-2013, 12:42 PM.

  • #2
    Solved by removing cuffData.db from directory.

    Comment


    • #3
      Dear all,
      any suggestion about this issue I have?

      I run the following commands:
      > library (cummeRbund)
      Loading required package: RSQLite
      Loading required package: DBI
      Loading required package: ggplot2
      Loading required package: reshape2
      > cuff<-readCufflinks ()
      > cuff
      CuffSet instance with:
      2 samples
      24302 genes
      42262 isoforms
      28828 TSS
      25037 CDS
      24302 promoters
      28828 splicing
      0 relCDS
      > iso.diff <- diffData(isoforms(cuff))
      > iso.diff.top <- iso.diff[order(iso.diff$q_value),][1:20,]
      > iso.diff.top
      isoform_id sample_1 sample_2 status value_1 value_2
      19598 TCONS_00019647 q1 q2 OK 0.00142518 63.8030
      23003 TCONS_00023056 q1 q2 OK 0.01873000 267.5380
      16085 TCONS_00016126 q1 q2 OK 0.00828880 53.7744
      20375 TCONS_00020425 q1 q2 OK 0.01018440 41.0838
      14718 TCONS_00014757 q1 q2 OK 0.01255110 52.7526
      38909 TCONS_00038994 q1 q2 OK 0.00506554 18.4579
      9364 TCONS_00009383 q1 q2 OK 0.01624700 41.5996
      21567 TCONS_00021617 q1 q2 OK 0.02047770 43.5210
      21617 TCONS_00021668 q1 q2 OK 0.07737150 173.5400
      12908 TCONS_00012945 q1 q2 OK 0.01454510 29.1976
      2916 TCONS_00002919 q1 q2 OK 0.02808040 52.5176
      11888 TCONS_00011918 q1 q2 OK 0.01283370 23.4124
      24967 TCONS_00025024 q1 q2 OK 0.07871780 93.7237
      36578 TCONS_00036659 q1 q2 OK 0.15108000 179.3100
      18827 TCONS_00018874 q1 q2 OK 0.19685300 402.2040
      26748 TCONS_00026809 q1 q2 OK 0.07271350 66.3874
      24573 TCONS_00024628 q1 q2 OK 0.01203420 20.7750
      5805 TCONS_00005818 q1 q2 OK 0.00198928 2.9240
      35808 TCONS_00035884 q1 q2 OK 0.10710700 108.1710
      26864 TCONS_00026926 q1 q2 OK 0.05353970 86.0766
      log2_fold_change test_stat p_value q_value significant
      19598 15.45020 -7.91793 2.44249e-15 5.34124e-11 yes
      23003 13.80210 -7.39372 1.42775e-13 1.56110e-09 yes
      16085 12.66350 -7.33093 2.28484e-13 1.66550e-09 yes
      20375 11.97800 -7.27264 3.52607e-13 1.92770e-09 yes
      14718 12.03720 -7.23914 4.51417e-13 1.97432e-09 yes
      38909 11.83120 -7.17187 7.39853e-13 2.69652e-09 yes
      9364 11.32220 -6.84004 7.91722e-12 2.47334e-08 yes
      21567 11.05340 -6.73898 1.59504e-11 3.87558e-08 yes
      21617 11.13120 -6.75063 1.47207e-11 3.87558e-08 yes
      12908 10.97110 -6.67956 2.39653e-11 5.24073e-08 yes
      2916 10.86900 -6.61070 3.82498e-11 6.62383e-08 yes
      11888 10.83310 -6.59542 4.24061e-11 6.62383e-08 yes
      24967 10.21750 -6.60852 3.88183e-11 6.62383e-08 yes
      36578 10.21290 -6.59690 4.19833e-11 6.62383e-08 yes
      18827 10.99660 -6.54690 5.87441e-11 8.56411e-08 yes
      26748 9.83447 -6.44433 1.16116e-10 1.58701e-07 yes
      24573 10.75350 -6.42860 1.28785e-10 1.65663e-07 yes
      5805 10.52150 -6.40323 1.52120e-10 1.84809e-07 yes
      35808 9.98005 -6.39398 1.61620e-10 1.86017e-07 yes
      26864 10.65080 -6.35030 2.14901e-10 2.34972e-07 yes


      however, these top 20 include transcripts that start with NM_00000 and NR_00000

      what I want is to select only the NM_ as these are proteins/transcript, NR_ if I am not wrong is the gene (here cummerbund only gives TCONS, but I have double checked themn with the NM/NR nomenclature and I know they are mixed up as it is listing by fold change...)

      How do I command this on cummerbund?

      thanks,
      ibseq

      Comment

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