Cummerbund: Error in data.frame arguments imply differing number of rows

Question

[Doom]

Hi, I analysed some RNA-seq data with Galaxy, I was using cummeRbund on R to do some clustering and I realized that some genes are disappearing from the clusters. If I use the specific genes that "disappear" I am getting an error:

> myGeneIds<- c("TNF","RELB")                               #genes OK
> myGenes <- getGenes(cuff_data,myGeneIds)
Getting gene information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting isoforms information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting CDS information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting TSS information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting promoter information:
    distData
Getting splicing information:
    distData
Getting relCDS information:
    distData
Warning messages:
1: Closing open result set, pending rows 
2: Closing open result set, pending rows 
> h<-csHeatmap(myGenes)
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
> h
> myGeneIds2<- c("CCL15","ARNT2")                                #missing genes
> myGenes2 <- getGenes(cuff_data,myGeneIds2)
Getting gene information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting isoforms information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting CDS information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting TSS information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting promoter information:
    distData
Getting splicing information:
    distData
Getting relCDS information:
    distData
Warning messages:
1: Closing open result set, pending rows 
2: Closing open result set, pending rows 
> h2<-csHeatmap(myGenes2)
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 8, 0

Answer 1

[handgabriel]

I'm also getting the same error for every gene in my sqlite file (also produced on Galaxy) when I try to use cummeRbund in a local R instance.

Is anyone able to successfully call genes from an sqlite file produced by Galaxy's cuffdiff? There may be a larger issue here.