[BioC] arrayQualityMetrics

[Al Ivens]

Hi Audrey,

Thanks for the prompt reply.  I take your point about split.plots,
although sometimes it IS useful to see everything together!  Could the
html report perhaps have a separate graphic with the legend, which might
thus get around the "space on the plot" issue?

Cheers and thanks,

a

> -----Original Message-----
> From: audrey [mailto:audrey at ebi.ac.uk] 
> Sent: 19 December 2007 09:03
> To: Al Ivens
> Cc: 'bioc'
> Subject: Re: [BioC] arrayQualityMetrics
> 
> 
> Hi Al,
> 
> Thank you for the useful feedback. In the development version of 
> arrayQualityMetrics, I have added a legend with the name of the 
> experiments on the density and ecdf plots. I will think about 
> adding the 
> same on the RNAdeg plot in the next version.
> However when there are too many experiments there is not 
> enough place on 
> the plot to write all the experiment names so I advice you in 
> that case 
> to use the argument "split.plots" of arrayQualityMetrics and 
> to set it 
> at 20 maximum.
> 
> Thank you,
> Audrey
> 
> 
> Al Ivens wrote:
> > Hi,
> >
> > I have been using arrayQualityMetrics, and find it very useful. 
> > However, to make it even more useful, would it be possible to have 
> > legends for some of the plots, e.g. density/ecdf, RNAdeg 
> incorporated 
> > in the output?
> >
> > Cheers and thanks,
> >
> > a
> >
> >
> >   
> >> sessionInfo()
> >>     
> > R version 2.6.0 (2007-10-03)
> > i386-pc-mingw32 
> >
> > locale:
> > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> > Kingdom.1252;LC_MONETARY=English_United
> > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> >
> > attached base packages:
> >  [1] grid      splines   tools     stats     graphics  
> grDevices utils
> > datasets  methods   base     
> >
> > other attached packages:
> >  [1] arrayQualityMetrics_1.2.0 latticeExtra_0.3-1        CCl4_1.0.6
> > simpleaffy_2.14.05       
> >  [5] affyPLM_1.14.0            gcrma_2.10.0
> > matchprobes_1.10.0        RColorBrewer_1.0-2       
> >  [9] vsn_3.2.1                 limma_2.12.0              affy_1.16.0
> > preprocessCore_1.0.0     
> > [13] affyio_1.6.1              genefilter_1.16.0         
> survival_2.34
> > geneplotter_1.16.0       
> > [17] lattice_0.17-2            annotate_1.16.1           
> xtable_1.5-2
> > AnnotationDbi_1.0.6      
> > [21] RSQLite_0.6-4             DBI_0.2-4                 
> Biobase_1.16.1
> >
> >
> > loaded via a namespace (and not attached):
> > [1] KernSmooth_2.22-21
> >   
> >
> >
> >
> >
> >   
> 




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