Hi Petr,
Please try keep threads on the bioconductor mailing list so that others may benefit from the answers provided.

The issue here is that your sample names are integers and R will not allow integers to be used as column names in a data.frame.  The easiest solution is to re-run your cuffdiff analysis using labels for your samples that do not start with a numeric value (0-9).

Best of luck!

-Loyal

On May 7, 2014, at 10:31 AM, Petr Broz <bbrozpetr@gmail.com> wrote:

> The naming was just numbers - 7510,7511,7512,7877.
> 
> Petr.
> 
> 
> On Wed, May 7, 2014 at 4:21 PM, Petr Broz <bbrozpetr@gmail.com> wrote:
> Dear Loyal,
> 
> thank you for very fast response. I used newest Tophat - 2.0.11 and for cufflinks and cuffmerge 2.2.0 and for cuffdiff 2.2.1 (I found newest version just today of cufflinks). But I had the absolutely same problem when I used the version cufflinks 2.2.0 for all analysis one week ago. 
> 
> Here is session info:
> 
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] grid      parallel  stats     graphics  grDevices utils     datasets 
> [8] methods   base     
> 
> other attached packages:
>  [1] cummeRbund_2.5.3      Gviz_1.7.10           rtracklayer_1.23.22  
>  [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30  IRanges_1.21.44      
>  [7] fastcluster_1.1.13    reshape2_1.2.2        ggplot2_0.9.3.1      
> [10] RSQLite_0.11.4        DBI_0.2-7             BiocGenerics_0.9.3   
> 
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.25.17     BatchJobs_1.2            
>  [3] BBmisc_1.5                Biobase_2.23.6           
>  [5] BiocParallel_0.5.20       biomaRt_2.19.3           
>  [7] Biostrings_2.31.22        biovizBase_1.11.15       
>  [9] bitops_1.0-6              brew_1.0-6               
> [11] BSgenome_1.31.13          cluster_1.15.2           
> [13] codetools_0.2-8           colorspace_1.2-4         
> [15] dichromat_2.0-0           digest_0.6.4             
> [17] fail_1.2                  foreach_1.4.1            
> [19] Formula_1.1-1             GenomicAlignments_0.99.38
> [21] GenomicFeatures_1.15.15   gtable_0.1.2             
> [23] Hmisc_3.14-3              iterators_1.0.6          
> [25] labeling_0.2              lattice_0.20-29          
> [27] latticeExtra_0.6-26       MASS_7.3-31              
> [29] matrixStats_0.8.14        munsell_0.4.2            
> [31] plyr_1.8.1                proto_0.3-10             
> [33] RColorBrewer_1.0-5        Rcpp_0.11.1              
> [35] RCurl_1.95-4.1            R.methodsS3_1.6.1        
> [37] Rsamtools_1.15.41         scales_0.2.3             
> [39] sendmailR_1.1-2           splines_3.1.0            
> [41] stats4_3.1.0              stringr_0.6.2            
> [43] survival_2.37-7           tools_3.1.0              
> [45] VariantAnnotation_1.9.49  XML_3.98-1.1             
> [47] XVector_0.3.7             zlibbioc_1.9.0 
> 
> Thank you for help,
> 
> Petr.
> 
> 
> On Wed, May 7, 2014 at 4:07 PM, Loyal A. Goff <lgoff@csail.mit.edu> wrote:
> Also,
> Can you tell me what the sample names were in your experiment? It may be relevant to why the DB build failed.
> 
> Loyal
> 
> Sent from my iPad
> 
> > On May 7, 2014, at 8:44 AM, Petr [guest] <guest@bioconductor.org> wrote:
> >
> >
> > Dear Bioconductor Team,
> >
> > after I running TopHat - Cufflinks - Cuffmerge - Cuffdiff and try to create plots with cummeRbund I have trouble with importing my data. I follow protocol from Nature (Differential gene transcripts expression analysis of RNA-seq experiment with TopHat and Cufflinks). I use gtf file downloaded from iGenomes. When I wants plot some basic graphs it is work - csDensity,csBoxplot..But some doesnt work - expressionBarplot,fpkmSCVPlot... I am paste down my codes.
> >
> > I found on internet the same issue but without any good solutions.
> >
> > Thank you so much,
> >
> > Petr.
> >
> > -- output of sessionInfo():
> >
> >> cuff <- readCufflinks()
> > Creating database /home/iab/CUSTOMERS/HiSeq/Dr.Susor/mouse_rna/all_samples_diff/cuffData.db
> > Reading Run Info File /home/iab/CUSTOMERS/HiSeq/Dr.Susor/mouse_rna/all_samples_diff/run.info
> > Writing runInfo Table
> > Reading Read Group Info  /home/iab/CUSTOMERS/HiSeq/Dr.Susor/mouse_rna/all_samples_diff/read_groups.info
> > Writing replicates Table
> > Reading /home/iab/CUSTOMERS/HiSeq/Dr.Susor/mouse_rna/all_samples_diff/genes.fpkm_tracking
> > Checking samples table...
> > Populating samples table...
> > Writing genes table
> > Reshaping geneData table
> > Recasting
> > Writing geneData table
> > Reading /home/iab/CUSTOMERS/HiSeq/Dr.Susor/mouse_rna/all_samples_diff/gene_exp.diff
> > Error in (function (classes, fdef, mtable)  :
> >  unable to find an inherited method for function ‘make.db.names’ for signature ‘"SQLiteConnection", "integer"’
> >> cuff
> > Error: object 'cuff' not found
> >> cuff <- readCufflinks()
> > dir=           gtfFile=       repTableFile=  geneDiff=      geneRep=       isoformDiff=   isoformRep=    TSSDiff=       TSSRep=        CDSExpDiff=    CDSRep=        promoterFile=  driver=        rebuild=       ...=
> > dbFile=        runInfoFile=   geneFPKM=      geneCount=     isoformFPKM=   isoformCount=  TSSFPKM=       TSSCount=      CDSFPKM=       CDSCount=      CDSDiff=       splicingFile=  genome=        verbose=
> >> cuff <- readCufflinks()
> >> cuff
> > CuffSet instance with:
> >     4 samples
> >     23235 genes
> >     0 isoforms
> >     0 TSS
> >     0 CDS
> >     0 promoters
> >     0 splicing
> >     0 relCDS
> >
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> 
> 


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