[BioC] CummeRbund getGenes command broken in R?
Zain A Alvi
zain.alvi at student.shu.edu
Fri Mar 7 04:47:50 CET 2014
Dear Dr. Goff,
I hope this reaches you well. Thank you so much for the quick reply. I just checked everything, the myGeneIds contained two gene_short_names and I tried the common gene_ids from the same server where I acquired the *.FastA and *.gtf files. The same FastA and gtf files were used during previous parts of the Tuxedo package.
I just tried again with gene_ids, but this time I copied for the specific genes from the gene_exp.diff file. I think there was small difference between server ids for the genes versus the gene_exp.diff file.
Sorry for such a novice mistake. I really appreciate the fast reply and help.
From: Loyal A. Goff <lgoff at csail.mit.edu>
Sent: Thursday, March 06, 2014 9:45 PM
To: Zain Alvi [guest]
Cc: bioconductor at r-project.org; Zain A Alvi
Subject: Re: CummeRbund getGenes command broken in R?
Please confirm that MyGeneIds is a non-empty vector that contains valid gene ids or gene_short_names...
Loyal A. Goff
CSAIL, MIT &
> On Mar 6, 2014, at 8:10 PM, Zain Alvi [guest] <guest at bioconductor.org> wrote:
> 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
> Sent via the guest posting facility at bioconductor.org.
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