[BioC] Problem CummeRbund

[Loyal A. Goff]

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 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.