Hi, I have experianced mutliple errors when plotting using cummerbund 2.0 but only some functions, and it works on the demo dataset. My is data from replicates and density plots works - dens(), but not the densrep() function, can this be a problem of the cuffdiff version? Here is also session info: R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.1 cummeRbund_2.0.0 Gviz_1.2.0 rtracklayer_1.18.0 GenomicRanges_1.10.1 [6] IRanges_1.16.2 fastcluster_1.1.7 reshape2_1.2.1 ggplot2_0.9.2.1 RSQLite_0.11.2 [11] DBI_0.2-5 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.0 BSgenome_1.26.0 Biobase_2.18.0 Biostrings_2.26.1 [5] GenomicFeatures_1.10.0 Hmisc_3.9-3 MASS_7.3-22 RColorBrewer_1.0-5 [9] RCurl_1.95-0.1.2 Rsamtools_1.10.1 XML_3.95-0.1 biomaRt_2.14.0 [13] biovizBase_1.6.0 bitops_1.0-4.1 cluster_1.14.2 colorspace_1.1-1 [17] dichromat_1.2-4 digest_0.5.2 gtable_0.1.1 labeling_0.1 [21] lattice_0.20-10 memoise_0.1 munsell_0.4 parallel_2.15.1 [25] plyr_1.7.1 proto_0.3-9.2 scales_0.2.2 stats4_2.15.1 [29] stringr_0.6.1 tools_2.15.1 zlibbioc_1.4.0 -- output of sessionInfo(): > disp<-dispersionPlot(genes(cuff)) > disp Error in layout_base(data, vars, drop = drop) : Faceting variables must have at least one value > genes.scv<-fpkmSCVPlot(genes(cuff)) Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near ")": syntax error) > isoforms.scv<-fpkmSCVPlot(isoforms(cuff)) Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near ")": syntax error) > densRep<-csDensity(genes(cuff),replicates=T) Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near ")": syntax err -- Sent via the guest posting facility at bioconductor.org.

hard to check at the moment, I'll ask our admin; but unfortunately, it's rather an old version as this on galaxy i tried cuff<-readCufflinks(rebuild=T), the same problem Creating database /Users/mbi/Desktop/RNAseq/cummerbund/replicatesnew/cuffData.db Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: database is locked) On Mon, Oct 8, 2012 at 6:17 PM, Loyal A. Goff <lgoff@csail.mit.edu> wrote: > The new version of cummerbund is designed to work with cuffdiff >=2.0.0, > and therefore if you have a cuffdiff analysis generated prior to cuffdiff > 2.0, there may be some functionality that is not available. > > Are you working on a dataset that you had previously used with an earlier > version of cummerbund? There have been a few changes to the underlying DB > schema for one, and it is always a good idea when you update cummerbund to > rebuild the database backend on previous analyses: > > cuff<-readCufflinks(rebuild=T) > > This will adjust the schema accordingly, and if you do have the relevant > output from cuffdiff2, this will now be integrated into the cuffData.db > backend. > > The error that you are getting from dispersionPlot() suggests to me that > there may not be the pertinent information from cuffdiff2 available in your > output.. > > What version of cuffdiff was used to generate your output? > > -Loyal > > > On Oct 8, 2012, at 11:53 AM, Micheal [guest] <guest@bioconductor.org> > wrote: > > > > > Hi, > > > > I have experianced mutliple errors when plotting using cummerbund 2.0 > but only some functions, and it works on the demo dataset. > > > > My is data from replicates and density plots works - dens(), but not the > densrep() function, can this be a problem of the cuffdiff version? > > > > Here is also session info: > > > > R version 2.15.1 (2012-06-22) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] C/en_US.UTF-8/C/C/C/C > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > base > > > > other attached packages: > > [1] BiocInstaller_1.8.1 cummeRbund_2.0.0 Gviz_1.2.0 > rtracklayer_1.18.0 GenomicRanges_1.10.1 > > [6] IRanges_1.16.2 fastcluster_1.1.7 reshape2_1.2.1 > ggplot2_0.9.2.1 RSQLite_0.11.2 > > [11] DBI_0.2-5 BiocGenerics_0.4.0 > > > > loaded via a namespace (and not attached): > > [1] AnnotationDbi_1.20.0 BSgenome_1.26.0 Biobase_2.18.0 > Biostrings_2.26.1 > > [5] GenomicFeatures_1.10.0 Hmisc_3.9-3 MASS_7.3-22 > RColorBrewer_1.0-5 > > [9] RCurl_1.95-0.1.2 Rsamtools_1.10.1 XML_3.95-0.1 > biomaRt_2.14.0 > > [13] biovizBase_1.6.0 bitops_1.0-4.1 cluster_1.14.2 > colorspace_1.1-1 > > [17] dichromat_1.2-4 digest_0.5.2 gtable_0.1.1 > labeling_0.1 > > [21] lattice_0.20-10 memoise_0.1 munsell_0.4 > parallel_2.15.1 > > [25] plyr_1.7.1 proto_0.3-9.2 scales_0.2.2 > stats4_2.15.1 > > [29] stringr_0.6.1 tools_2.15.1 zlibbioc_1.4.0 > > > > -- output of sessionInfo(): > > > >> disp<-dispersionPlot(genes(cuff)) > >> disp > > Error in layout_base(data, vars, drop = drop) : > > Faceting variables must have at least one value > > > >> genes.scv<-fpkmSCVPlot(genes(cuff)) > > Error in sqliteExecStatement(con, statement, bind.data) : > > RS-DBI driver: (error in statement: near ")": syntax error) > >> isoforms.scv<-fpkmSCVPlot(isoforms(cuff)) > > Error in sqliteExecStatement(con, statement, bind.data) : > > RS-DBI driver: (error in statement: near ")": syntax error) > > > >> densRep<-csDensity(genes(cuff),replicates=T) > > Error in sqliteExecStatement(con, statement, bind.data) : > > RS-DBI driver: (error in statement: near ")": syntax err > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > [[alternative HTML version deleted]]

> Actually this is now a different problem in that your database is > locked You may want to try to move the cuffData.db file to a different > location (keep it as a backup) and then try to rebuild. > Sorry, I wasn't precise enough I tried it before but no change. I'll try with the new version, I hope I can still use the old transcript assemblies from cufflinks-1.3 :) Thanks for help! > My guess is that you are using an older version. I would highly recommend > that you run the most recent version of cuffdiff if possible, for numerous > reasons, least of which is compatibility with the new cummerbund. > > Cheers, > Loyal > > On Oct 8, 2012, at 12:35 PM, Michael <mllmmllmmllmm@gmail.com> wrote: > > hard to check at the moment, I'll ask our admin; but unfortunately, it's > rather an old version as this on galaxy > > i tried cuff<-readCufflinks(rebuild=T), the same problem > > > Creating database > /Users/mbi/Desktop/RNAseq/cummerbund/replicatesnew/cuffData.db > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: database is locked) > > > > On Mon, Oct 8, 2012 at 6:17 PM, Loyal A. Goff <lgoff@csail.mit.edu> wrote: > >> The new version of cummerbund is designed to work with cuffdiff >=2.0.0, >> and therefore if you have a cuffdiff analysis generated prior to cuffdiff >> 2.0, there may be some functionality that is not available. >> >> Are you working on a dataset that you had previously used with an earlier >> version of cummerbund? There have been a few changes to the underlying DB >> schema for one, and it is always a good idea when you update cummerbund to >> rebuild the database backend on previous analyses: >> >> cuff<-readCufflinks(rebuild=T) >> >> This will adjust the schema accordingly, and if you do have the relevant >> output from cuffdiff2, this will now be integrated into the cuffData.db >> backend. >> >> The error that you are getting from dispersionPlot() suggests to me that >> there may not be the pertinent information from cuffdiff2 available in your >> output.. >> >> What version of cuffdiff was used to generate your output? >> >> -Loyal >> >> >> On Oct 8, 2012, at 11:53 AM, Micheal [guest] <guest@bioconductor.org> >> wrote: >> >> > >> > Hi, >> > >> > I have experianced mutliple errors when plotting using cummerbund 2.0 >> but only some functions, and it works on the demo dataset. >> > >> > My is data from replicates and density plots works - dens(), but not >> the densrep() function, can this be a problem of the cuffdiff version? >> > >> > Here is also session info: >> > >> > R version 2.15.1 (2012-06-22) >> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> > >> > locale: >> > [1] C/en_US.UTF-8/C/C/C/C >> > >> > attached base packages: >> > [1] grid stats graphics grDevices utils datasets methods >> base >> > >> > other attached packages: >> > [1] BiocInstaller_1.8.1 cummeRbund_2.0.0 Gviz_1.2.0 >> rtracklayer_1.18.0 GenomicRanges_1.10.1 >> > [6] IRanges_1.16.2 fastcluster_1.1.7 reshape2_1.2.1 >> ggplot2_0.9.2.1 RSQLite_0.11.2 >> > [11] DBI_0.2-5 BiocGenerics_0.4.0 >> > >> > loaded via a namespace (and not attached): >> > [1] AnnotationDbi_1.20.0 BSgenome_1.26.0 Biobase_2.18.0 >> Biostrings_2.26.1 >> > [5] GenomicFeatures_1.10.0 Hmisc_3.9-3 MASS_7.3-22 >> RColorBrewer_1.0-5 >> > [9] RCurl_1.95-0.1.2 Rsamtools_1.10.1 XML_3.95-0.1 >> biomaRt_2.14.0 >> > [13] biovizBase_1.6.0 bitops_1.0-4.1 cluster_1.14.2 >> colorspace_1.1-1 >> > [17] dichromat_1.2-4 digest_0.5.2 gtable_0.1.1 >> labeling_0.1 >> > [21] lattice_0.20-10 memoise_0.1 munsell_0.4 >> parallel_2.15.1 >> > [25] plyr_1.7.1 proto_0.3-9.2 scales_0.2.2 >> stats4_2.15.1 >> > [29] stringr_0.6.1 tools_2.15.1 zlibbioc_1.4.0 >> > >> > -- output of sessionInfo(): >> > >> >> disp<-dispersionPlot(genes(cuff)) >> >> disp >> > Error in layout_base(data, vars, drop = drop) : >> > Faceting variables must have at least one value >> > >> >> genes.scv<-fpkmSCVPlot(genes(cuff)) >> > Error in sqliteExecStatement(con, statement, bind.data) : >> > RS-DBI driver: (error in statement: near ")": syntax error) >> >> isoforms.scv<-fpkmSCVPlot(isoforms(cuff)) >> > Error in sqliteExecStatement(con, statement, bind.data) : >> > RS-DBI driver: (error in statement: near ")": syntax error) >> > >> >> densRep<-csDensity(genes(cuff),replicates=T) >> > Error in sqliteExecStatement(con, statement, bind.data) : >> > RS-DBI driver: (error in statement: near ")": syntax err >> > >> > -- >> > Sent via the guest posting facility at bioconductor.org. >> >> > > [[alternative HTML version deleted]]