[BioC] Error when doing RNA deg plot on Estrogen data.

[Keith Satterley]

Hi Paul,

If I remember rightly there are some zero values in the Estrogen data and when 
logs are taken you get infinite values - not good for plotting!

In the affylmGUI package, I ask whether you wish to log the values for this very 
reason as I used the Estrogen data as my example data. When not logging the 
values, the RNAdeg plot works, so your problem is data specific, not a problem 
with the R code.

cheers,

Keith

========================
Keith Satterley
affylmGUI Maintainer
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
=======================

Paul Geeleher wrote:
> Hi,
> 
> I'm trying to plot RNA degradation of the Estrogen dataset, using the
> following commands:
> 
> RNAdeg <- AffyRNAdeg(abatch)
> plotAffyRNAdeg(RNAdeg)
> 
> But I'm recieving the following error:
> 
> 'Error in plot.window(...) : need finite 'ylim' values'
> 
> I'm using the latest version of R and Bioconductor on SUSE Linux and
> the commands seem to run fine on other datasets.
> 
> Any ideas why this could be or what this is about?
> 
> Thanks,
> 
> -Paul.
> 
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