[BioC] CummeRbund getGenes command broken in R?
Zain Alvi [guest]
guest at bioconductor.org
Fri Mar 7 02:10:36 CET 2014
Dear Sir or Madam,
I hope this reaches you well. I have been working with R and cummeRbund for the past few months. Everything seemed to be fine with the getGenes command in the manual.
Apparently, today when I was trying to create a heatmap for my genes of interest. I would get the following error no matter what I have do:
> myGenes <- getGenes(cuff,myGeneIds)
Getting gene information:
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)
I am using latest version of cummeRbund with R. Also my Cuffdiff output was done through Cufflinks/Cuffmerge/Cuffdiff 2.0.2.
I checked my old data, which has worked in the past and I received the same error, which is strange.
Also I have reinstalled cummeRbund as well. I've rebuilt the database file as well. No matter, what I do I get this same error.
If you could kindly help me. I would really appreciate it.
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:
 grid parallel stats graphics grDevices utils datasets methods base
other attached packages:
 cummeRbund_2.4.1 Gviz_1.6.0 rtracklayer_1.22.4 GenomicRanges_1.14.4
 XVector_0.2.0 IRanges_1.20.7 fastcluster_1.1.13 reshape2_1.2.2
 ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
 AnnotationDbi_1.24.0 Biobase_2.22.0 biomaRt_2.18.0 Biostrings_2.30.1
 biovizBase_1.10.8 bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4
 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 Formula_1.1-1
 GenomicFeatures_1.14.3 gtable_0.1.2 Hmisc_3.14-3 labeling_0.2
 lattice_0.20-23 latticeExtra_0.6-26 MASS_7.3-29 munsell_0.4.2
 plyr_1.8.1 proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.0
 RCurl_1.95-4.1 Rsamtools_1.14.3 scales_0.2.3 splines_3.0.2
 stats4_3.0.2 stringr_0.6.2 survival_2.37-7 tools_3.0.2
 XML_3.98-1.1 zlibbioc_1.8.0
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