All,
I was trying to create a dendrogram (including replicates) in cummeRbund using the csDendro function, but I get an error stating: "Error in plot.window(...) : need finite 'ylim' values". I'm using the following command:
Does anyone know why?
Useful information:
Thanks for your help!
I was trying to create a dendrogram (including replicates) in cummeRbund using the csDendro function, but I get an error stating: "Error in plot.window(...) : need finite 'ylim' values". I'm using the following command:
Code:
cuff<-readCufflinks() dend.rep<-csDendro(genes(cuff),replicates=T)
Does anyone know why?
Useful information:
- I'm using R 2.15.1, tophat2 2.0.3, cufflinks 2.0.2, and cummeRbund 1.99.2
- I have been following the protocol from Nature Protocols (http://www.nature.com/nprot/journal/....2012.016.html), but I'm getting a lot of NOTEST results (49,956) from cuffdiff. I'm currently awaiting results from two test runs testing '-c 0' and '--min-outlier-p 0' to see if that helps with the NOTEST results and to see if it's related to the above cummeRbund error. I'm testing these parameters as per Cole Trapnell's suggestions (http://seqanswers.com/forums/showthr...merbund&page=2)
- I have two conditions with 30 and 23 replicates (mostly biological but a few technical)
Thanks for your help!
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