Question: Trouble plotting dispersion with CummeRbund R pack
gravatar for roy.granit
5.8 years ago by
roy.granit830 wrote:

Hello all,

I started using the CummeRbund R pack and find it very useful- yet I have been getting some errors while trying to plot  'dispersionPlot' & 'fpkmSCVPlot' (all the rest work just fine).

I am using R3.1.1 and used output of cuffdiff 2.2.1.

These are the errors I get:

> cuff

CuffSet instance with:
 6 samples
 63653 genes
 214292 isoforms
 0 TSS
 0 CDS
 0 promoters
 0 splicing
 0 relCDS

> disp<-dispersionPlot(genes(cuff))

> disp

Error in `$<`(`*tmp*`, "SCALE_X", value = 1L) : 

  replacement has 1 row, data has 0

In addition: Warning message:

In max(panels$ROW) : no non-missing arguments to max; returning -Inf

and the second error

> genes.scv<-fpkmSCVPlot(genes(cuff))

Error in sqliteExecStatement(con, statement, : 

RS-DBI driver: (error in statement: near ")": syntax error)


Any suggestions?



rna-seq cuffdiff cummerbund R • 2.0k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by roy.granit830
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