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. Sincerely, Zain ________________________________________ From: Loyal A. Goff <lgoff@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? Hi zain, Please confirm that MyGeneIds is a non-empty vector that contains valid gene ids or gene_short_names... Thanks, Loyal ------------------ Loyal A. Goff Postdoctoral Fellow CSAIL, MIT & SCRB, Harvard > 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: > FPKM > 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. > > Sincerely, > > Zain > > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] cummeRbund_2.4.1 Gviz_1.6.0 rtracklayer_1.22.4 GenomicRanges_1.14.4 > [5] XVector_0.2.0 IRanges_1.20.7 fastcluster_1.1.13 reshape2_1.2.2 > [9] ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.24.0 Biobase_2.22.0 biomaRt_2.18.0 Biostrings_2.30.1 > [5] biovizBase_1.10.8 bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 > [9] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 Formula_1.1-1 > [13] GenomicFeatures_1.14.3 gtable_0.1.2 Hmisc_3.14-3 labeling_0.2 > [17] lattice_0.20-23 latticeExtra_0.6-26 MASS_7.3-29 munsell_0.4.2 > [21] plyr_1.8.1 proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.0 > [25] RCurl_1.95-4.1 Rsamtools_1.14.3 scales_0.2.3 splines_3.0.2 > [29] stats4_3.0.2 stringr_0.6.2 survival_2.37-7 tools_3.0.2 > [33] XML_3.98-1.1 zlibbioc_1.8.0 > > -- > Sent via the guest posting facility at bioconductor.org.