Entering edit mode
6.5 years ago
Doom
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10
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