[BioC] cummeRbund issues

[Loyal A. Goff]

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.
> 
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