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  • cummeRbund error

    Hi guys!
    I am trying to create a geneSet with cummeRbund to analyze my RNAseq data (2 samples, no replicates).

    This is the error message:
    > myGenes <- getGenes(cuff, myGeneIds)
    Error in sqliteExecStatement(conn, statement, ...) :
    RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

    What does it mean?
    more: I have Ensembl annotation, thus my gene list is "ENSG...", but when writing
    > data(sampleData)
    > myGeneIds <- sampleIDs
    > myGeneIds
    [1] "XLOC_001363" "XLOC_001297" "XLOC_001339" "XLOC_000132" "XLOC_001265" "XLOC_000151" "XLOC_001359" "XLOC_000069" "XLOC_000170" "XLOC_000105" "XLOC_001262"
    [12] "XLOC_001348" "XLOC_001411" "XLOC_001369" "XLOC_000158" "XLOC_001370" "XLOC_001263" "XLOC_000115" "XLOC_000089" "XLOC_001240"

    is this normal?
    Hope someone could help!
    Thanks
    Manu

    R version 3.0.1 (2013-05-16)
    Platform: x86_64-apple-darwin10.8.0 (64-bit)

    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] splines grid parallel stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] cummeRbund_2.2.0 Hmisc_3.10-1.1 survival_2.37-4 Gviz_1.4.2 rtracklayer_1.20.2 GenomicRanges_1.12.4 IRanges_1.18.1
    [8] BiocGenerics_0.6.0 fastcluster_1.1.11 plyr_1.8 reshape2_1.2.2 ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7
    [15] BiocInstaller_1.10.2

    loaded via a namespace (and not attached):
    [1] AnnotationDbi_1.22.6 Biobase_2.20.0 biomaRt_2.16.0 Biostrings_2.28.0 biovizBase_1.8.1 bitops_1.0-5 BSgenome_1.28.0
    [8] cluster_1.14.4 colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.12.2 gtable_0.1.2 labeling_0.1
    [15] lattice_0.20-15 MASS_7.3-26 munsell_0.4 proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.12.3
    [22] scales_0.2.3 stats4_3.0.1 stringr_0.6.2 tools_3.0.1 XML_3.95-0.2 zlibbioc_1.6.0

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