[BioC] Problem CummeRbund

[Loyal A. Goff]

Hi petr,
Your cummerbund database is not fully built ( as indicated by the first 'error' in your pasted code), but the database was initialized and at least one table populated.  Subsequent calls to readCufflinks are establishing connections to the malformed database, but the data required to generated the plots have not been incorporated.  First things first, we need to figure out why your database did not build correctly.

Can you please paste the results of a call to sessionInfo(), and elaborate on what version of cufflinks/cuff diff was used to process your reads?

Loyal


Sent from my iPad

> On May 7, 2014, at 8:44 AM, Petr [guest] <guest at 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.