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Old 06-15-2013, 11:41 AM   #1
Location: New haven

Join Date: May 2013
Posts: 47
Default 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!

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

[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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