Question: cummeRbund help - getGenes
0
gravatar for jcfleming.ent
3.5 years ago by
United Kingdom
jcfleming.ent0 wrote:

Hi all,
really appreciate if anyone can help with this.
I have XLOC gene names in my cuffdiff output (despite always using annotation in previous steps) and I have been trying to convert to gene names to allow intrepretation, using the solution as posted in http://seqanswers.com/forums/showthr...light=getGenes with getGenes() function

However I keep getting the following error

PHP Code:


> cuff <- readCufflinks('diff_out1/')
> diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05)
> is.vector(diffGeneIDs)
[1] TRUE
> diffGenes <- getGenes(cuff,diffGeneIDs)
Error in as.character.default(unlist(x)) : 
  no method for coercing this S4 class to a vector 


Hopefully it is a simple solution but Id really appreciate some help as I have ground to a halt!
BW
J

rna-seq • 1.2k views
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