[BioC] cummeRbund issues
Loyal A. Goff
lgoff at csail.mit.edu
Tue Aug 7 12:40:29 CEST 2012
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 A. Goff
CSAIL, MIT &
On Aug 7, 2012, at 6:27 AM, "irene [guest]" <guest at bioconductor.org> wrote:
> 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.
> -- output of sessionInfo():
>> library (cummeRbund)
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: ggplot2
> Loading required package: reshape2
> CuffSet instance with:
> 2 samples
> 24300 genes
> 0 isoforms
> 0 TSS
> 0 CDS
> 0 promoters
> 0 splicing
> 0 relCDS
> 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
> 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"
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