[BioC] cummeRbund issues

irene [guest] guest at bioconductor.org
Tue Aug 7 12:27:36 CEST 2012

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
> 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
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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