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  • cummeRbund csScatter() error

    Hello
    Can you please help me find out why I am getting this error? Thanks

    cuff = readCufflinks()
    > cuff
    CuffSet instance with:
    3 samples
    14017 genes
    32101 isoforms
    19668 TSS
    18380 CDS
    14017 promoters
    39336 splicing
    12808 relCDS

    The functions csVolcanoMatrix() and csDensity() work fine, but the function csScatter() gives the following error:
    Code:
    > csScatter(genes(cuff))
    Error in sqliteSendQuery(con, statement, bind.data) : 
      error in statement: near "OR": syntax error
    OR is the name of one of the 3 samples.


    > sessionInfo()
    R version 3.1.2 Patched (2015-01-19 r67548)
    Platform: x86_64-apple-darwin10.8.0 (64-bit)
    Running under: OS X 10.6.8 (Snow Leopard)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

    attached base packages:
    [1] grid stats4 parallel stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] cummeRbund_2.8.2 Gviz_1.10.5 rtracklayer_1.26.2 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4 IRanges_2.0.1 S4Vectors_0.4.0
    [8] fastcluster_1.1.15 reshape2_1.4.1 ggplot2_1.0.0 RSQLite_1.0.0 DBI_0.3.1 BiocGenerics_0.12.1

    loaded via a namespace (and not attached):
    [1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 Biobase_2.26.0
    [7] BiocParallel_1.0.0 biomaRt_2.22.0 Biostrings_2.34.1 biovizBase_1.14.1 bitops_1.0-6 brew_1.0-6
    [13] BSgenome_1.34.1 checkmate_1.5.1 cluster_1.15.3 codetools_0.2-10 colorspace_1.2-4 dichromat_2.0-0
    [19] digest_0.6.8 fail_1.2 foreach_1.4.2 foreign_0.8-62 Formula_1.2-0 GenomicAlignments_1.2.1
    [25] GenomicFeatures_1.18.3 gtable_0.1.2 Hmisc_3.14-6 iterators_1.0.7 labeling_0.3 lattice_0.20-29
    [31] latticeExtra_0.6-26 MASS_7.3-37 matrixStats_0.12.2 munsell_0.4.2 nnet_7.3-8 plyr_1.8.1
    [37] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.1-2 Rcpp_0.11.3 RCurl_1.95-4.5 rpart_4.1-8
    [43] Rsamtools_1.18.2 scales_0.2.4 sendmailR_1.2-1 splines_3.1.2 stringr_0.6.2 survival_2.37-7
    [49] tools_3.1.2 VariantAnnotation_1.12.8 XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0

  • #2
    Maybe your sample name is conflicted with the SQL syntax. Try to add another name for your sample.

    Comment


    • #3
      cs.scattermatrix error

      Originally posted by joseph View Post
      Hello
      Can you please help me find out why I am getting this error? Thanks

      cuff = readCufflinks()
      > cuff
      CuffSet instance with:
      3 samples
      14017 genes
      32101 isoforms
      19668 TSS
      18380 CDS
      14017 promoters
      39336 splicing
      12808 relCDS

      The functions csVolcanoMatrix() and csDensity() work fine, but the function csScatter() gives the following error:
      Code:
      > csScatter(genes(cuff))
      Error in sqliteSendQuery(con, statement, bind.data) : 
        error in statement: near "OR": syntax error
      OR is the name of one of the 3 samples.


      > sessionInfo()
      R version 3.1.2 Patched (2015-01-19 r67548)
      Platform: x86_64-apple-darwin10.8.0 (64-bit)
      Running under: OS X 10.6.8 (Snow Leopard)

      locale:
      [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

      attached base packages:
      [1] grid stats4 parallel stats graphics grDevices utils datasets methods base

      other attached packages:
      [1] cummeRbund_2.8.2 Gviz_1.10.5 rtracklayer_1.26.2 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4 IRanges_2.0.1 S4Vectors_0.4.0
      [8] fastcluster_1.1.15 reshape2_1.4.1 ggplot2_1.0.0 RSQLite_1.0.0 DBI_0.3.1 BiocGenerics_0.12.1

      loaded via a namespace (and not attached):
      [1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 Biobase_2.26.0
      [7] BiocParallel_1.0.0 biomaRt_2.22.0 Biostrings_2.34.1 biovizBase_1.14.1 bitops_1.0-6 brew_1.0-6
      [13] BSgenome_1.34.1 checkmate_1.5.1 cluster_1.15.3 codetools_0.2-10 colorspace_1.2-4 dichromat_2.0-0
      [19] digest_0.6.8 fail_1.2 foreach_1.4.2 foreign_0.8-62 Formula_1.2-0 GenomicAlignments_1.2.1
      [25] GenomicFeatures_1.18.3 gtable_0.1.2 Hmisc_3.14-6 iterators_1.0.7 labeling_0.3 lattice_0.20-29
      [31] latticeExtra_0.6-26 MASS_7.3-37 matrixStats_0.12.2 munsell_0.4.2 nnet_7.3-8 plyr_1.8.1
      [37] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.1-2 Rcpp_0.11.3 RCurl_1.95-4.5 rpart_4.1-8
      [43] Rsamtools_1.18.2 scales_0.2.4 sendmailR_1.2-1 splines_3.1.2 stringr_0.6.2 survival_2.37-7
      [49] tools_3.1.2 VariantAnnotation_1.12.8 XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0
      Dear Jozeph,

      I am now encountered with the same error as you were. Did you find a way to solve your problem? I would be so grateful if you share that with me.

      Thanks in advance'
      Karim

      Comment

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