Question: Trouble plotting dispersion with CummeRbund R pack
0
gravatar for roy.granit
5.2 years ago by
roy.granit800
Israel/LabWorm
roy.granit800 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 `$<-.data.frame`(`*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, bind.data) : 

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

 

Any suggestions?

Thanks!

 

rna-seq cuffdiff cummerbund R • 1.8k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by roy.granit800
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