[BioC] Problem CummeRbund

[Petr [guest]]

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


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