Hi, I am recently using the cummeRbund package of R and have the folllowing issue: I have 8 otjer samples and they all run fine, with none 0 values. Any help is much appreciated. Thanks! Irene -- output of sessionInfo(): > library (cummeRbund) Loading required package: RSQLite Loading required package: DBI Loading required package: ggplot2 Loading required package: reshape2 > cuff<-readCufflinks() > cuff CuffSet instance with: 2 samples 24300 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS > cuff<-readCufflinks(rebuild=T) Creating database /home/bsib/ibcl/cuffData.db Reading /home/bsib/ibcl/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading /home/bsib/ibcl/gene_exp.diff Error in function (classes, fdef, mtable) : unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "NULL" -- Sent via the guest posting facility at bioconductor.org.

Hi Irene, What are the sample names for your cuffdiff run? (ie what was the -L argument?). This problem usually results from using non R-friendly sample names in the cuffdiff run. Loyal ------------------ Loyal A. Goff Postdoctoral Fellow CSAIL, MIT & SCRB, Harvard On Aug 7, 2012, at 6:27 AM, "irene [guest]" <guest at="" bioconductor.org=""> wrote: > > Hi, > I am recently using the cummeRbund package of R and have the folllowing issue: > > I have 8 otjer samples and they all run fine, with none 0 values. > > Any help is much appreciated. > > Thanks! > Irene > > -- output of sessionInfo(): > >> library (cummeRbund) > Loading required package: RSQLite > Loading required package: DBI > Loading required package: ggplot2 > Loading required package: reshape2 >> cuff<-readCufflinks() >> cuff > CuffSet instance with: > 2 samples > 24300 genes > 0 isoforms > 0 TSS > 0 CDS > 0 promoters > 0 splicing > 0 relCDS >> cuff<-readCufflinks(rebuild=T) > Creating database /home/bsib/ibcl/cuffData.db > Reading /home/bsib/ibcl/genes.fpkm_tracking > Checking samples table... > Populating samples table... > Writing genes table > Reshaping geneData table > Recasting > Writing geneData table > Reading /home/bsib/ibcl/gene_exp.diff > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "NULL" > > > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor